genome.wustl.edu.TCGA-A1-A0SD.snv.0e81f9c986154ce89e59240c3f09534f.txt 174 KB
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#version 2.4
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	Exon_Number	t_depth	t_ref_count	t_alt_count	n_depth	n_ref_count	n_alt_count	all_effects	Allele	Gene	Feature	Feature_type	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	ALLELE_NUM	DISTANCE	STRAND_VEP	SYMBOL	SYMBOL_SOURCE	HGNC_ID	BIOTYPE	CANONICAL	CCDS	ENSP	SWISSPROT	TREMBL	UNIPARC	RefSeq	SIFT	PolyPhen	EXON	INTRON	DOMAINS	AF	AFR_AF	AMR_AF	ASN_AF	EAS_AF	EUR_AF	SAS_AF	AA_AF	EA_AF	CLIN_SIG	SOMATIC	PUBMED	MOTIF_NAME	MOTIF_POS	HIGH_INF_POS	MOTIF_SCORE_CHANGE	IMPACT	PICK	VARIANT_CLASS	TSL	HGVS_OFFSET	PHENO	MINIMISED	ExAC_AF	ExAC_AF_AFR	ExAC_AF_AMR	ExAC_AF_EAS	ExAC_AF_FIN	ExAC_AF_NFE	ExAC_AF_OTH	ExAC_AF_SAS	GENE_PHENO	FILTER	flanking_bps	vcf_id	vcf_qual	ExAC_AF_Adj	ExAC_AC_AN_Adj	ExAC_AC_AN	ExAC_AC_AN_AFR	ExAC_AC_AN_AMR	ExAC_AC_AN_EAS	ExAC_AC_AN_FIN	ExAC_AC_AN_NFE	ExAC_AC_AN_OTH	ExAC_AC_AN_SAS	ExAC_FILTER	gnomAD_AF	gnomAD_AFR_AF	gnomAD_AMR_AF	gnomAD_ASJ_AF	gnomAD_EAS_AF	gnomAD_FIN_AF	gnomAD_NFE_AF	gnomAD_OTH_AF	gnomAD_SAS_AF	vcf_pos
FAM213B	127281	.	GRCh37	1	2520302	2520302	+	Intron	SNP	T	T	C	rs6667564		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.551-59T>C			ENST00000419916		9	4	5	5			FAM213B,intron_variant,,ENST00000378424,;FAM213B,intron_variant,,ENST00000378425,;FAM213B,intron_variant,,ENST00000378427,NM_001195737.1,NM_001195738.1;FAM213B,intron_variant,,ENST00000419916,NM_152371.3;FAM213B,intron_variant,,ENST00000444521,NM_001195736.1;FAM213B,intron_variant,,ENST00000465233,;FAM213B,intron_variant,,ENST00000498083,;FAM213B,intron_variant,,ENST00000537325,NM_001195740.1,NM_001195741.1;MMEL1,downstream_gene_variant,,ENST00000288709,NM_033467.3;MMEL1,downstream_gene_variant,,ENST00000378412,;MMEL1,downstream_gene_variant,,ENST00000471840,;MMEL1,downstream_gene_variant,,ENST00000502556,;RP3-395M20.9,downstream_gene_variant,,ENST00000424215,;FAM213B,non_coding_transcript_exon_variant,,ENST00000476686,;FAM213B,intron_variant,,ENST00000464043,;FAM213B,intron_variant,,ENST00000474659,;FAM213B,intron_variant,,ENST00000481683,;FAM213B,intron_variant,,ENST00000484099,;FAM213B,intron_variant,,ENST00000493183,;FAM213B,downstream_gene_variant,,ENST00000477045,;MMEL1,downstream_gene_variant,,ENST00000464195,;MMEL1,downstream_gene_variant,,ENST00000469962,;MMEL1,downstream_gene_variant,,ENST00000491941,;MMEL1,downstream_gene_variant,,ENST00000504800,;	C	ENSG00000157870	ENST00000419916	Transcript	intron_variant						rs6667564	1		1	FAM213B	HGNC	28390	protein_coding	YES	CCDS44.2	ENSP00000394405		J3KQD0	UPI0001E306A4	NM_152371.3				5/6		0.5607	0.8041	0.4885		0.5427	0.333	0.5358										MODIFIER	1	SNV														.	ATG	.	.																					2520302
RERE	473	.	GRCh37	1	8421092	8421092	+	Silent	SNP	C	C	T	rs2784735		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.2475G>A	p.Pro825=	p.P825=	ENST00000337907	19/24	11	3	7	6			RERE,synonymous_variant,p.Pro825=,ENST00000337907,NM_012102.3;RERE,synonymous_variant,p.Pro557=,ENST00000377464,;RERE,synonymous_variant,p.Pro825=,ENST00000400908,NM_001042681.1;RERE,synonymous_variant,p.Pro271=,ENST00000476556,NM_001042682.1;RERE,intron_variant,,ENST00000400907,;RERE,intron_variant,,ENST00000505225,;RERE,downstream_gene_variant,,ENST00000488215,;RERE,downstream_gene_variant,,ENST00000460659,;RERE,downstream_gene_variant,,ENST00000465125,;RERE,downstream_gene_variant,,ENST00000492766,;RERE,downstream_gene_variant,,ENST00000464367,;	T	ENSG00000142599	ENST00000337907	Transcript	synonymous_variant	3110/8026	2475/4701	825/1566	P	ccG/ccA	rs2784735,COSV61936274	1		-1	RERE	HGNC	9965	protein_coding	YES	CCDS95.1	ENSP00000338629	Q9P2R6	K7EJQ1,K7EIQ4,K7EIE3	UPI00001419CC	NM_012102.3			19/24		Low_complexity_(Seg):seg,PANTHER:PTHR13859,PANTHER:PTHR13859:SF12,Pfam:PF03154	0.4579	0.1899	0.5115		0.8353	0.4553	0.3957	0.2015	0.3898		0,1						LOW	1	SNV			0,1										1	.	GCG	.	.												0.5019	0.2182	0.5448	0.4756	0.8413	0.4342	0.4657	0.5109	0.4115	8421092
FAM131C	348487	.	GRCh37	1	16386416	16386416	+	Silent	SNP	G	G	A	rs9442230		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.399C>T	p.Asp133=	p.D133=	ENST00000375662	5/7	30	11	19	8			FAM131C,synonymous_variant,p.Asp133=,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,non_coding_transcript_exon_variant,,ENST00000494078,;	A	ENSG00000185519	ENST00000375662	Transcript	synonymous_variant	583/1695	399/843	133/280	D	gaC/gaT	rs9442230	1		-1	FAM131C	HGNC	26717	protein_coding	YES	CCDS41270.1	ENSP00000364814	Q96AQ9		UPI000022B016	NM_182623.2			5/7		Pfam:PF15010,PANTHER:PTHR15736:SF2,PANTHER:PTHR15736	0.7105	0.4871	0.768		0.8155	0.7584	0.8139	0.5421	0.7568								LOW	1	SNV														.	CGT	.	.												0.7541	0.506	0.8603	0.7568	0.8079	0.6489	0.7505	0.7625	0.8094	16386416
EPHA2	1969	.	GRCh37	1	16464673	16464673	+	Silent	SNP	G	G	A	rs2230597		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.987C>T	p.Pro329=	p.P329=	ENST00000358432	5/17	15	3	12	6			EPHA2,synonymous_variant,p.Pro329=,ENST00000358432,NM_004431.3;EPHA2,non_coding_transcript_exon_variant,,ENST00000480202,;EPHA2,upstream_gene_variant,,ENST00000462805,;	A	ENSG00000142627	ENST00000358432	Transcript	synonymous_variant	1142/3964	987/2931	329/976	P	ccC/ccT	rs2230597	1		-1	EPHA2	HGNC	3386	protein_coding	YES	CCDS169.1	ENSP00000351209	P29317	Q96HF4,Q8IZL0	UPI00000731AB	NM_004431.3			5/17		Gene3D:2.60.40.10,PIRSF:PIRSF000666,PROSITE_profiles:PS50853,PANTHER:PTHR24416,PANTHER:PTHR24416:SF306,SMART:SM00060,Superfamily:SSF49265,Superfamily:SSF57184	0.3494	0.3396	0.4294		0.1458	0.4215	0.4417	0.3606	0.4032	benign		25741868,26996484,19649315,20361013,27626691					LOW	1	SNV			1										1	.	AGG	.	.												0.377	0.3509	0.3595	0.4478	0.1261	0.3469	0.4019	0.4011	0.459	16464673
CROCCP2	84809	.	GRCh37	1	16974869	16974869	+	5'Flank	SNP	G	G	C	rs4570422		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																			ENST00000362058		17	11	6	4			CROCCP2,upstream_gene_variant,,ENST00000362058,;MST1P2,non_coding_transcript_exon_variant,,ENST00000334429,;MST1P2,non_coding_transcript_exon_variant,,ENST00000457982,;MST1P2,non_coding_transcript_exon_variant,,ENST00000418421,;	C	ENSG00000215908	ENST00000362058	Transcript	upstream_gene_variant						rs4570422	1	3691	-1	CROCCP2	HGNC	28170	retained_intron	YES																												MODIFIER		SNV														.	GGG	.	.																					16974869
CNKSR1	10256	.	GRCh37	1	26504108	26504108	+	Intron	SNP	A	A	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.52+18A>T			ENST00000361530		183	141	42	219	216	1	CNKSR1,intron_variant,,ENST00000361530,;CNKSR1,intron_variant,,ENST00000374253,NM_006314.2;CNKSR1,upstream_gene_variant,,ENST00000531191,;CNKSR1,intron_variant,,ENST00000480348,;CNKSR1,upstream_gene_variant,,ENST00000528001,;CNKSR1,intron_variant,,ENST00000465415,;CNKSR1,intron_variant,,ENST00000481077,;CNKSR1,intron_variant,,ENST00000482227,;CNKSR1,intron_variant,,ENST00000525687,;CNKSR1,upstream_gene_variant,,ENST00000524529,;CNKSR1,upstream_gene_variant,,ENST00000531150,;,regulatory_region_variant,,ENSR00000925171,;	T	ENSG00000142675	ENST00000361530	Transcript	intron_variant							1		1	CNKSR1	HGNC	19700	protein_coding	YES	CCDS276.1	ENSP00000354609	Q969H4	Q53GM7,G3V160	UPI0000366501					1/20																		MODIFIER	1	SNV													1	.	TAG	.	.																					26504108
MACF1	23499	.	GRCh37	1	39796854	39796854	+	Intron	SNP	T	T	C	rs922560079		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.4629+3829T>C			ENST00000545844		15	11	4	19			MACF1,5_prime_UTR_variant,,ENST00000289893,;MACF1,intron_variant,,ENST00000317713,;MACF1,intron_variant,,ENST00000361689,NM_012090.5;MACF1,intron_variant,,ENST00000372915,;MACF1,intron_variant,,ENST00000372925,;MACF1,intron_variant,,ENST00000530262,;MACF1,intron_variant,,ENST00000539005,;MACF1,intron_variant,,ENST00000545844,;MACF1,intron_variant,,ENST00000564288,;MACF1,intron_variant,,ENST00000567887,;MACF1,intron_variant,,ENST00000476350,;MACF1,intron_variant,,ENST00000528611,;MACF1,downstream_gene_variant,,ENST00000496804,;	C	ENSG00000127603	ENST00000545844	Transcript	intron_variant						rs922560079	1		1	MACF1	HGNC	13664	protein_coding	YES	CCDS435.1	ENSP00000439537	Q9UPN3	Q8WXY4,Q8WXY3,Q8WXY0,Q8WXX9,B4DNC4	UPI00001B3DC6					36/93																		MODIFIER	1	SNV													1	.	TTT	.	.																					39796854
PCSK9	255738	.	GRCh37	1	55505732	55505732	+	Intron	SNP	A	A	G	rs2495482		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.207+15A>G			ENST00000302118		14	4	10	4			PCSK9,intron_variant,,ENST00000302118,NM_174936.3;PCSK9,intron_variant,,ENST00000452118,;PCSK9,upstream_gene_variant,,ENST00000543384,;,regulatory_region_variant,,ENSR00000931854,;	G	ENSG00000169174	ENST00000302118	Transcript	intron_variant						rs2495482	1		1	PCSK9	HGNC	20001	protein_coding	YES	CCDS603.1	ENSP00000303208	Q8NBP7		UPI00001615E1	NM_174936.3				1/11		0.9086	0.8101	0.8818		0.9444	0.9493	0.9816	0.8397	0.9484	benign,benign/likely_benign,likely_benign		25741868					MODIFIER	1	SNV			1										1	.	GAT	.	.												0.9278	0.8303	0.8359	0.9278	0.9405	0.9651	0.9512	0.942	0.9703	55505732
MTF2	22823	.	GRCh37	1	93599238	93599238	+	Intron	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.1161-22G>T			ENST00000370298		29	26	3	47	47	0	MTF2,intron_variant,,ENST00000370298,NM_007358.3,NM_001164392.1;MTF2,intron_variant,,ENST00000370303,;MTF2,intron_variant,,ENST00000540243,NM_001164393.1;MTF2,intron_variant,,ENST00000545708,NM_001164391.1;MTF2,intron_variant,,ENST00000467953,;MTF2,intron_variant,,ENST00000471953,;MTF2,intron_variant,,ENST00000476037,;MTF2,intron_variant,,ENST00000487263,;MTF2,intron_variant,,ENST00000489480,;MTF2,intron_variant,,ENST00000497976,;	T	ENSG00000143033	ENST00000370298	Transcript	intron_variant							1		1	MTF2	HGNC	29535	protein_coding	YES	CCDS742.1	ENSP00000359321	Q9Y483		UPI0000205B55	NM_007358.3,NM_001164392.1				11/14																		MODIFIER	1	SNV														.	TGC	.	.																					93599238
SLC44A3	126969	.	GRCh37	1	95293148	95293148	+	Missense_Mutation	SNP	G	G	A			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.364G>A	p.Glu122Lys	p.E122K	ENST00000271227	4/15	266	197	69	176	176	0	SLC44A3,missense_variant,p.Glu122Lys,ENST00000271227,NM_001258340.1,NM_001114106.2,NM_001258341.1;SLC44A3,missense_variant,p.Glu86Lys,ENST00000446120,NM_001258342.1;SLC44A3,missense_variant,p.Glu74Lys,ENST00000467909,NM_152369.4;SLC44A3,missense_variant,p.Glu74Lys,ENST00000422520,;SLC44A3,intron_variant,,ENST00000527077,NM_001258343.1;SLC44A3,intron_variant,,ENST00000529450,;SLC44A3,intron_variant,,ENST00000532427,;SLC44A3,intron_variant,,ENST00000530397,;SLC44A3,3_prime_UTR_variant,,ENST00000475883,;	A	ENSG00000143036	ENST00000271227	Transcript	missense_variant	466/2388	364/1962	122/653	E/K	Gaa/Aaa	COSV54733731	1		1	SLC44A3	HGNC	28689	protein_coding	YES	CCDS44176.1	ENSP00000271227	Q8N4M1	F8W7F3	UPI0000206066	NM_001258340.1,NM_001114106.2,NM_001258341.1	tolerated(0.28)	benign(0.388)	4/15		PANTHER:PTHR12385,PANTHER:PTHR12385:SF13											1						MODERATE	1	SNV			1											.	TGA	.	.																					95293148
DDX20	11218	.	GRCh37	1	112305406	112305406	+	Splice_Site	SNP	T	T	A	rs1164121575		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1210+2T>A		p.X404_splice	ENST00000369702		147	134	9	194	184	7	DDX20,splice_donor_variant,,ENST00000369702,NM_007204.4;DDX20,splice_donor_variant,,ENST00000536167,;DDX20,5_prime_UTR_variant,,ENST00000475700,;DDX20,splice_donor_variant,,ENST00000533164,;DDX20,splice_donor_variant,,ENST00000534200,;DDX20,downstream_gene_variant,,ENST00000524894,;	A	ENSG00000064703	ENST00000369702	Transcript	splice_donor_variant						rs1164121575	1		1	DDX20	HGNC	2743	protein_coding	YES	CCDS842.1	ENSP00000358716	Q9UHI6		UPI0000129080	NM_007204.4				9/10																		HIGH	1	SNV														.	GTA	.	.																					112305406
CASQ2	845	.	GRCh37	1	116268198	116268198	+	Intron	SNP	A	A	G	rs922752705		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.738-24T>C			ENST00000261448		61	56	5	63	63	0	CASQ2,intron_variant,,ENST00000261448,NM_001232.3;CASQ2,intron_variant,,ENST00000456138,;CASQ2,downstream_gene_variant,,ENST00000488931,;,regulatory_region_variant,,ENSR00001504305,;	G	ENSG00000118729	ENST00000261448	Transcript	intron_variant						rs922752705	1		-1	CASQ2	HGNC	1513	protein_coding	YES	CCDS884.1	ENSP00000261448	O14958		UPI0000126F16	NM_001232.3				6/10																		MODIFIER	1	SNV													1	.	AAA	.	.												0.0001725		6.101e-05		6.015e-05	0.0002317	0.0002375		0.0002786	116268198
HMGCS2	3158	.	GRCh37	1	120296069	120296069	+	Intron	SNP	C	C	T	rs200470161		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1188-60G>A			ENST00000369406		19	14	5	30			HMGCS2,intron_variant,,ENST00000369406,NM_005518.3;HMGCS2,intron_variant,,ENST00000544913,NM_001166107.1;HMGCS2,downstream_gene_variant,,ENST00000472375,;HMGCS2,downstream_gene_variant,,ENST00000476640,;	T	ENSG00000134240	ENST00000369406	Transcript	intron_variant						rs200470161,COSV65569544	1		-1	HMGCS2	HGNC	5008	protein_coding	YES	CCDS905.1	ENSP00000358414	P54868		UPI000000DA7A	NM_005518.3				6/9												0,1						MODIFIER	1	SNV			0,1										1	.	ACA	.	.																					120296069
PDE4DIP	9659	.	GRCh37	1	144994654	144994654	+	Silent	SNP	G	G	A	rs147804991		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.78C>T	p.Ile26=	p.I26=	ENST00000369356	1/44	347	291	55	168			PDE4DIP,synonymous_variant,p.Ile163=,ENST00000369359,;PDE4DIP,synonymous_variant,p.Ile26=,ENST00000369356,NM_014644.5,NM_001198834.3;PDE4DIP,synonymous_variant,p.Ile163=,ENST00000530740,;PDE4DIP,synonymous_variant,p.Ile26=,ENST00000369354,;PDE4DIP,synonymous_variant,p.Ile92=,ENST00000313382,NM_001198832.2;PDE4DIP,synonymous_variant,p.Ile26=,ENST00000369351,;PDE4DIP,synonymous_variant,p.Ile26=,ENST00000369349,NM_001002812.2;PDE4DIP,synonymous_variant,p.Ile163=,ENST00000369348,NM_022359.5;PDE4DIP,synonymous_variant,p.Ile26=,ENST00000369347,NM_001002810.3,NM_001195260.1;PDE4DIP,synonymous_variant,p.Ile29=,ENST00000534536,;PDE4DIP,synonymous_variant,p.Ile93=,ENST00000531369,;PDE4DIP,intron_variant,,ENST00000532801,;PDE4DIP,intron_variant,,ENST00000533259,;AL590452.1,downstream_gene_variant,,ENST00000596396,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000532803,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000528552,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000533163,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000497529,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000533396,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000530472,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000464103,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000533845,;PDE4DIP,synonymous_variant,p.Ile43=,ENST00000496572,;PDE4DIP,synonymous_variant,p.Ile26=,ENST00000526445,;PDE4DIP,synonymous_variant,p.Ile92=,ENST00000530822,;PDE4DIP,synonymous_variant,p.Ile29=,ENST00000528129,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000527063,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000530078,;,regulatory_region_variant,,ENSR00000944941,;	A	ENSG00000178104	ENST00000369356	Transcript	synonymous_variant	369/8307	78/7089	26/2362	I	atC/atT	rs147804991	1		-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	Q5VU43	I1VE15	UPI0000458A81	NM_014644.5,NM_001198834.3			1/44		Pfam:PF07989,PANTHER:PTHR13895,PANTHER:PTHR13895:SF2								0.0009079	0.001628								LOW	1	SNV													1	.	AGA	.	.												0.001395	0.0003109	0.000118	0.0002041		0.001398	0.00166	0.001023	0.003966	144994654
PDE4DIP	9659	.	GRCh37	1	144994861	144994861	+	5'UTR	SNP	C	T	T	rs2442640		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.-130G>A			ENST00000369356	1/44	41	6	35	47			PDE4DIP,5_prime_UTR_variant,,ENST00000369356,NM_014644.5,NM_001198834.3;PDE4DIP,5_prime_UTR_variant,,ENST00000369354,;PDE4DIP,5_prime_UTR_variant,,ENST00000369349,NM_001002812.2;PDE4DIP,5_prime_UTR_variant,,ENST00000369347,NM_001002810.3,NM_001195260.1;PDE4DIP,intron_variant,,ENST00000313382,NM_001198832.2;PDE4DIP,intron_variant,,ENST00000369348,NM_022359.5;PDE4DIP,intron_variant,,ENST00000369359,;PDE4DIP,intron_variant,,ENST00000530740,;PDE4DIP,intron_variant,,ENST00000531369,;PDE4DIP,intron_variant,,ENST00000532801,;PDE4DIP,intron_variant,,ENST00000533259,;PDE4DIP,intron_variant,,ENST00000534536,;PDE4DIP,upstream_gene_variant,,ENST00000369351,;AL590452.1,downstream_gene_variant,,ENST00000596396,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000530472,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000533845,;PDE4DIP,intron_variant,,ENST00000464103,;PDE4DIP,intron_variant,,ENST00000497529,;PDE4DIP,intron_variant,,ENST00000528552,;PDE4DIP,intron_variant,,ENST00000532803,;PDE4DIP,intron_variant,,ENST00000533163,;PDE4DIP,intron_variant,,ENST00000533396,;PDE4DIP,5_prime_UTR_variant,,ENST00000526445,;PDE4DIP,intron_variant,,ENST00000496572,;PDE4DIP,intron_variant,,ENST00000527063,;PDE4DIP,intron_variant,,ENST00000528129,;PDE4DIP,intron_variant,,ENST00000530078,;PDE4DIP,intron_variant,,ENST00000530822,;	T	ENSG00000178104	ENST00000369356	Transcript	5_prime_UTR_variant	162/8307					rs2442640	1		-1	PDE4DIP	HGNC	15580	protein_coding	YES	CCDS55627.1	ENSP00000358363	Q5VU43	I1VE15	UPI0000458A81	NM_014644.5,NM_001198834.3			1/44																			MODIFIER	1	SNV													1	.	ACG	.	.																					144994861
NOTCH2NL	388677	.	GRCh37	1	145273431	145273431	+	Silent	SNP	A	A	G	rs1132928		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.285A>G	p.Gln95=	p.Q95=	ENST00000369340	4/6	960	833	127	385			NOTCH2NL,synonymous_variant,p.Gln95=,ENST00000369340,;NOTCH2NL,synonymous_variant,p.Gln95=,ENST00000344859,;NOTCH2NL,synonymous_variant,p.Gln95=,ENST00000362074,NM_203458.4;RP11-458D21.5,synonymous_variant,p.Gln95=,ENST00000468030,;	G	ENSG00000213240	ENST00000369340	Transcript	synonymous_variant	729/5036	285/711	95/236	Q	caA/caG	rs1132928	1		1	NOTCH2NL	HGNC	31862	protein_coding	YES	CCDS909.1	ENSP00000358346	Q7Z3S9		UPI00001A9982				4/6		Gene3D:2.10.25.10,Pfam:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,PANTHER:PTHR24033,PANTHER:PTHR24033:SF43,SMART:SM00179,SMART:SM00181,Superfamily:SSF57196																	LOW	1	SNV														.	AAG	.	.												0.1177	0.2446	0.1196	0.05458	0.3916	0.08299	0.06447	0.0839	0.1585	145273431
CA14	23632	.	GRCh37	1	150230424	150230424	+	5'UTR	SNP	T	T	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.-100T>G			ENST00000369111	1/11	247	240	7	129	128	0	CA14,5_prime_UTR_variant,,ENST00000369111,NM_012113.1;snoU13,upstream_gene_variant,,ENST00000458929,;RP4-790G17.7,upstream_gene_variant,,ENST00000607002,;CA14,non_coding_transcript_exon_variant,,ENST00000607751,;CA14,non_coding_transcript_exon_variant,,ENST00000607652,;CA14,upstream_gene_variant,,ENST00000483993,;,regulatory_region_variant,,ENSR00001505636,;	G	ENSG00000118298	ENST00000369111	Transcript	5_prime_UTR_variant	871/2403						1		1	CA14	HGNC	1372	protein_coding	YES	CCDS947.1	ENSP00000358107	Q9ULX7	A8K3J4	UPI00000389EA	NM_012113.1			1/11																			MODIFIER	1	SNV														.	CTC	.	.																					150230424
LCE1C	353133	.	GRCh37	1	152777901	152777901	+	Silent	SNP	G	G	A	rs139259976		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.54C>T	p.Pro18=	p.P18=	ENST00000368768	2/2	241	219	22	112	112	0	LCE1C,synonymous_variant,p.Pro18=,ENST00000368768,NM_178351.3,NM_001276331.1;LCE1C,synonymous_variant,p.Pro18=,ENST00000607093,;LCE1C,intron_variant,,ENST00000606576,;	A	ENSG00000197084	ENST00000368768	Transcript	synonymous_variant	105/695	54/357	18/118	P	ccC/ccT	rs139259976	1		-1	LCE1C	HGNC	29464	protein_coding	YES	CCDS1026.1	ENSP00000357757	Q5T751		UPI0000140B0A	NM_178351.3,NM_001276331.1			2/2		Prints:PR00021,PANTHER:PTHR23263,PANTHER:PTHR23263:SF46,Low_complexity_(Seg):seg																	LOW	1	SNV														.	TGG	.	.																					152777901
LCE1C	353133	.	GRCh37	1	152777903	152777903	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.52C>G	p.Pro18Ala	p.P18A	ENST00000368768	2/2	234	214	20	112	112	0	LCE1C,missense_variant,p.Pro18Ala,ENST00000368768,NM_178351.3,NM_001276331.1;LCE1C,missense_variant,p.Pro18Ala,ENST00000607093,;LCE1C,splice_region_variant,,ENST00000606576,;	C	ENSG00000197084	ENST00000368768	Transcript	missense_variant	103/695	52/357	18/118	P/A	Ccc/Gcc		1		-1	LCE1C	HGNC	29464	protein_coding	YES	CCDS1026.1	ENSP00000357757	Q5T751		UPI0000140B0A	NM_178351.3,NM_001276331.1	deleterious_low_confidence(0)	probably_damaging(0.934)	2/2		Prints:PR00021,PANTHER:PTHR23263,PANTHER:PTHR23263:SF46,Low_complexity_(Seg):seg																	MODERATE	1	SNV														.	GGG	.	.																					152777903
KIRREL	55243	.	GRCh37	1	158054332	158054332	+	Missense_Mutation	SNP	G	G	A	rs191023947		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.473G>A	p.Arg158Gln	p.R158Q	ENST00000359209	4/15	159	112	47	41	41	0	KIRREL,missense_variant,p.Arg158Gln,ENST00000368173,NM_018240.5;KIRREL,missense_variant,p.Arg158Gln,ENST00000359209,;KIRREL,missense_variant,p.Arg58Gln,ENST00000416935,;KIRREL,intron_variant,,ENST00000360089,;KIRREL,intron_variant,,ENST00000392272,;KIRREL,upstream_gene_variant,,ENST00000368172,NM_001286349.1;	A	ENSG00000183853	ENST00000359209	Transcript	missense_variant	540/2874	473/2274	158/757	R/Q	cGg/cAg	rs191023947,COSV63291064	1		1	KIRREL	HGNC	15734	protein_coding	YES	CCDS1172.2	ENSP00000352138	Q96J84		UPI0000443FBD		deleterious(0.03)	possibly_damaging(0.572)	4/15		Gene3D:2.60.40.10,Pfam:PF08205,PROSITE_profiles:PS50835,PANTHER:PTHR11640,PANTHER:PTHR11640:SF14,SMART:SM00409,Superfamily:SSF48726	0.0002					0.001					0,1						MODERATE	1	SNV			0,1											.	CGG	.	.												1.929e-05						4.983e-05			158054332
PYHIN1	149628	.	GRCh37	1	158943328	158943328	+	Intron	SNP	T	T	C	rs12145823		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1360-109T>C			ENST00000368140		27	13	14	19			PYHIN1,intron_variant,,ENST00000368138,;PYHIN1,intron_variant,,ENST00000368140,NM_152501.4,NM_198928.4,NM_198929.4;PYHIN1,intron_variant,,ENST00000392252,NM_198930.3;PYHIN1,intron_variant,,ENST00000392254,;	C	ENSG00000163564	ENST00000368140	Transcript	intron_variant						rs12145823	1		1	PYHIN1	HGNC	28894	protein_coding	YES	CCDS1178.1	ENSP00000357122	Q6K0P9		UPI0000225618	NM_152501.4,NM_198928.4,NM_198929.4				7/8		0.3548	0.4039	0.3588		0.4058	0.2982	0.2914										MODIFIER	1	SNV														.	ATA	.	.																					158943328
IFI16	3428	.	GRCh37	1	159019487	159019487	+	Intron	SNP	C	C	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1498-1982C>A			ENST00000368131		148	95	53	134	134	0	IFI16,intron_variant,,ENST00000295809,;IFI16,intron_variant,,ENST00000340979,;IFI16,intron_variant,,ENST00000359709,NM_001206567.1;IFI16,intron_variant,,ENST00000368131,NM_005531.2;IFI16,intron_variant,,ENST00000368132,;IFI16,intron_variant,,ENST00000430894,;IFI16,intron_variant,,ENST00000448393,;IFI16,intron_variant,,ENST00000483916,;IFI16,intron_variant,,ENST00000493884,;IFI16,intron_variant,,ENST00000562225,;	A	ENSG00000163565	ENST00000368131	Transcript	intron_variant							1		1	IFI16	HGNC	5395	protein_coding	YES	CCDS1180.3	ENSP00000357113	Q16666	H3BVE6,H3BR88,H3BR65,H3BM18	UPI00001412C9	NM_005531.2				8/10																		MODIFIER	1	SNV														.	ACA	.	.																					159019487
DCAF8	50717	.	GRCh37	1	160210108	160210108	+	Silent	SNP	C	C	T			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.102G>A	p.Glu34=	p.E34=	ENST00000368073	4/14	125	100	25	63	60	0	DCAF8,synonymous_variant,p.Glu34=,ENST00000368073,;DCAF8,synonymous_variant,p.Glu34=,ENST00000326837,;DCAF8,synonymous_variant,p.Glu34=,ENST00000368074,NM_015726.3;DCAF8,synonymous_variant,p.Glu188=,ENST00000556710,;DCAF8,synonymous_variant,p.Glu188=,ENST00000608310,;DCAF8,synonymous_variant,p.Glu34=,ENST00000610139,;DCAF8,synonymous_variant,p.Glu34=,ENST00000475733,;DCAF8,synonymous_variant,p.Glu9=,ENST00000495887,;DCAF8,synonymous_variant,p.Glu246=,ENST00000485079,;DCAF8,synonymous_variant,p.Glu34=,ENST00000447377,;DCAF8,synonymous_variant,p.Glu34=,ENST00000407642,;DCAF8,synonymous_variant,p.Glu34=,ENST00000440682,;DCAF8,synonymous_variant,p.Glu34=,ENST00000419626,;DCAF8,synonymous_variant,p.Glu34=,ENST00000461888,;DCAF8,upstream_gene_variant,,ENST00000466253,;	T	ENSG00000132716	ENST00000368073	Transcript	synonymous_variant	537/4106	102/1794	34/597	E	gaG/gaA	COSV58785788	1		-1	DCAF8	HGNC	24891	protein_coding	YES	CCDS1200.1	ENSP00000357052	Q5TAQ9	Q5TAQ8,Q5TAQ7,Q5TAQ6,Q5TAQ5,B7Z8C9	UPI0000141A39				4/14													1						LOW	1	SNV			1										1	.	TCT	.	.																					160210108
RNASEL	6041	.	GRCh37	1	182544815	182544815	+	Intron	SNP	T	C	C	rs11807829		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	C																c.2040-102A>G			ENST00000367559		16	0	16	24			RNASEL,intron_variant,,ENST00000367559,NM_021133.3;RNASEL,intron_variant,,ENST00000444138,;RNASEL,downstream_gene_variant,,ENST00000539397,;,regulatory_region_variant,,ENSR00001509190,;,TF_binding_site_variant,,ENSM00522053080,;	C	ENSG00000135828	ENST00000367559	Transcript	intron_variant						rs11807829	1		-1	RNASEL	HGNC	10050	protein_coding	YES	CCDS1347.1	ENSP00000356530	Q05823		UPI000005339F	NM_021133.3				6/6		0.2776	0.1732	0.3415		0.2054	0.338	0.3855					19567509,23057767,21360564,18575592,20576793					MODIFIER	1	SNV													1	.	TTG	.	.																					182544815
REN	5972	.	GRCh37	1	204125468	204125468	+	Intron	SNP	A	A	T	rs1424220636		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.819-21T>A			ENST00000272190		32	14	5	37	24	0	REN,intron_variant,,ENST00000272190,NM_000537.3;REN,intron_variant,,ENST00000367195,;ETNK2,upstream_gene_variant,,ENST00000367199,;ETNK2,upstream_gene_variant,,ENST00000367201,;ETNK2,upstream_gene_variant,,ENST00000367202,NM_018208.2;ETNK2,upstream_gene_variant,,ENST00000429525,;,regulatory_region_variant,,ENSR00001511363,;	T	ENSG00000143839	ENST00000272190	Transcript	intron_variant						rs1424220636,COSV65818061	1		-1	REN	HGNC	9958	protein_coding	YES	CCDS30981.1	ENSP00000272190	P00797	Q9UQK5	UPI000000091F	NM_000537.3				7/9												0,1						MODIFIER	1	SNV			0,1										1	.	GAC	.	.												7.012e-05		0.0001357			5.613e-05	6.167e-05	0.0003821	7.492e-05	204125468
OR2T8	343172	.	GRCh37	1	248085124	248085124	+	Missense_Mutation	SNP	G	A	A	rs4590708		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	A																c.805G>A	p.Asp269Asn	p.D269N	ENST00000319968	1/1	303	61	242	163			OR2T8,missense_variant,p.Asp269Asn,ENST00000319968,NM_001005522.1;	A	ENSG00000177462	ENST00000319968	Transcript	missense_variant	805/939	805/939	269/312	D/N	Gac/Aac	rs4590708	1		1	OR2T8	HGNC	15020	protein_coding	YES	CCDS31100.1	ENSP00000326225	A6NH00		UPI00001999E3	NM_001005522.1	deleterious(0.01)	benign(0.415)	1/1		PROSITE_profiles:PS50262,PANTHER:PTHR26453,PANTHER:PTHR26453:SF147,Pfam:PF13853,Gene3D:1.20.1070.10,Superfamily:SSF81321	0.3504	0.2769	0.2709		0.5387	0.1998	0.4673	0.2524	0.2208								MODERATE	1	SNV														.	CGA	.	.												0.2835	0.2617	0.2629	0.1983	0.5565	0.2504	0.2165	0.2541	0.4605	248085124
OR2T27	403239	.	GRCh37	1	248814126	248814126	+	Silent	SNP	G	A	A	rs28418327		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	A																c.60C>T	p.Asn20=	p.N20=	ENST00000344889	1/1	276	39	237	235			OR2T27,synonymous_variant,p.Asn20=,ENST00000344889,NM_001001824.1;	A	ENSG00000187701	ENST00000344889	Transcript	synonymous_variant	60/954	60/954	20/317	N	aaC/aaT	rs28418327	1		-1	OR2T27	HGNC	31252	protein_coding	YES	CCDS31124.1	ENSP00000342008	Q8NH04		UPI000004F239	NM_001001824.1			1/1		PANTHER:PTHR26453:SF78,PANTHER:PTHR26453,Gene3D:1.20.1070.10,Superfamily:SSF81321																	LOW	1	SNV														.	CGT	.	.												0.5814	0.5566	0.6352	0.5263	0.8442	0.5666	0.5254	0.5504	0.6128	248814126
TPO	7173	.	GRCh37	2	1546414	1546414	+	3'UTR	SNP	T	T	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.*168T>C			ENST00000345913	17/17	64	48	16	90	90	0	TPO,3_prime_UTR_variant,,ENST00000422464,;TPO,3_prime_UTR_variant,,ENST00000345913,NM_000547.5;TPO,3_prime_UTR_variant,,ENST00000329066,NM_001206744.1;TPO,3_prime_UTR_variant,,ENST00000337415,;TPO,3_prime_UTR_variant,,ENST00000346956,NM_175721.3;TPO,3_prime_UTR_variant,,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,3_prime_UTR_variant,,ENST00000349624,;TPO,3_prime_UTR_variant,,ENST00000446278,;TPO,3_prime_UTR_variant,,ENST00000469607,;TPO,3_prime_UTR_variant,,ENST00000425083,;TPO,downstream_gene_variant,,ENST00000382198,NM_175722.3;AC144450.1,downstream_gene_variant,,ENST00000438247,;TPO,non_coding_transcript_exon_variant,,ENST00000497517,;TPO,downstream_gene_variant,,ENST00000479902,;	C	ENSG00000115705	ENST00000345913	Transcript	3_prime_UTR_variant	3061/3145						1		1	TPO	HGNC	12015	protein_coding	YES	CCDS1643.1	ENSP00000318820	P07202	Q53QT2,C9J511	UPI000013D480	NM_000547.5			17/17																			MODIFIER	1	SNV													1	.	ATA	.	.																					1546414
GRHL1	29841	.	GRCh37	2	10132119	10132119	+	Intron	SNP	T	T	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1322-16T>A			ENST00000324907		123	116	6	104	103	1	GRHL1,intron_variant,,ENST00000324883,;GRHL1,intron_variant,,ENST00000324907,NM_198182.2;GRHL1,intron_variant,,ENST00000405379,;GRHL1,upstream_gene_variant,,ENST00000480736,;GRHL1,intron_variant,,ENST00000464418,;GRHL1,intron_variant,,ENST00000472167,;,regulatory_region_variant,,ENSR00001167849,;,regulatory_region_variant,,ENSR00001615206,;	A	ENSG00000134317	ENST00000324907	Transcript	intron_variant							1		1	GRHL1	HGNC	17923	protein_coding	YES	CCDS33144.2	ENSP00000324693	Q9NZI5	F8WFB0,C9JYY8	UPI00001E0586	NM_198182.2				10/15																		MODIFIER	1	SNV														.	ATT	.	.																					10132119
CGREF1	10669	.	GRCh37	2	27324340	27324340	+	Silent	SNP	G	G	A	rs11893427		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.759C>T	p.Pro253=	p.P253=	ENST00000402394	6/6	78	59	19	44			CGREF1,synonymous_variant,p.Pro253=,ENST00000402394,NM_006569.5;CGREF1,synonymous_variant,p.Pro253=,ENST00000312734,;CGREF1,synonymous_variant,p.Pro375=,ENST00000404694,;CGREF1,synonymous_variant,p.Pro253=,ENST00000405600,NM_001166239.1;CGREF1,intron_variant,,ENST00000260595,;CGREF1,intron_variant,,ENST00000402550,NM_001166240.1;CGREF1,intron_variant,,ENST00000452318,NM_001166241.1;KHK,downstream_gene_variant,,ENST00000260598,NM_006488.2;KHK,downstream_gene_variant,,ENST00000260599,NM_000221.2;KHK,downstream_gene_variant,,ENST00000429697,;KHK,downstream_gene_variant,,ENST00000490823,;CGREF1,intron_variant,,ENST00000440612,;KHK,downstream_gene_variant,,ENST00000464371,;CGREF1,downstream_gene_variant,,ENST00000467539,;KHK,downstream_gene_variant,,ENST00000469936,;	A	ENSG00000138028	ENST00000402394	Transcript	synonymous_variant	1028/1902	759/957	253/318	P	ccC/ccT	rs11893427	1		-1	CGREF1	HGNC	16962	protein_coding	YES	CCDS33162.2	ENSP00000385452	Q99674		UPI000013D0EB	NM_006569.5			6/6		Low_complexity_(Seg):seg																	LOW	1	SNV														.	CGG	.	.												3.193e-05	0.0001207	0.0001956							27324340
IFT172	26160	.	GRCh37	2	27708021	27708021	+	Intron	SNP	G	G	A	rs1243517993		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.184-24C>T			ENST00000260570		243	236	7	206	203	3	IFT172,intron_variant,,ENST00000260570,NM_015662.1;IFT172,intron_variant,,ENST00000359466,;IFT172,intron_variant,,ENST00000416524,;IFT172,intron_variant,,ENST00000475476,;IFT172,intron_variant,,ENST00000476264,;IFT172,intron_variant,,ENST00000507184,;IFT172,intron_variant,,ENST00000511842,;	A	ENSG00000138002	ENST00000260570	Transcript	intron_variant						rs1243517993	1		-1	IFT172	HGNC	30391	protein_coding	YES	CCDS1755.1	ENSP00000260570	Q9UG01	H7C161	UPI0000353ABB	NM_015662.1				2/47																		MODIFIER	1	SNV													1	.	AGA	.	.												9.239e-06						1.958e-05			27708021
USP34	9736	.	GRCh37	2	61462928	61462928	+	Intron	SNP	G	G	A	rs543444369		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.7032+52C>T			ENST00000398571		131	126	5	96	95	0	USP34,intron_variant,,ENST00000398571,NM_014709.3;USP34,intron_variant,,ENST00000411912,;USP34,intron_variant,,ENST00000453734,;USP34,intron_variant,,ENST00000472706,;USP34,intron_variant,,ENST00000463046,;	A	ENSG00000115464	ENST00000398571	Transcript	intron_variant						rs543444369	1		-1	USP34	HGNC	20066	protein_coding	YES	CCDS42686.1	ENSP00000381577	Q70CQ2		UPI0000410E09	NM_014709.3				57/79		0.0006	0.0023															MODIFIER	1	SNV														.	GGA	.	.																					61462928
HK2	3099	.	GRCh37	2	75114839	75114839	+	Intron	SNP	A	A	G	rs2171385		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.2220-191A>G			ENST00000290573		9	4	5	4			HK2,intron_variant,,ENST00000290573,NM_000189.4;HK2,intron_variant,,ENST00000409174,;,regulatory_region_variant,,ENSR00001181622,;	G	ENSG00000159399	ENST00000290573	Transcript	intron_variant						rs2171385	1		1	HK2	HGNC	4923	protein_coding	YES	CCDS1956.1	ENSP00000290573	P52789	Q7Z7Q6,Q53SG7,Q53QX9,Q09LL6,E9PB90	UPI00000706E4	NM_000189.4				15/17		0.1791	0.2201	0.1599		0.1716	0.159	0.1656										MODIFIER	1	SNV														.	AAG	.	.																					75114839
SFTPB	6439	.	GRCh37	2	85890293	85890293	+	Intron	SNP	T	T	C	rs2118177		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1038+176A>G			ENST00000393822		8	2	6	4			SFTPB,intron_variant,,ENST00000342375,NM_000542.3,NM_198843.2;SFTPB,intron_variant,,ENST00000393822,;SFTPB,intron_variant,,ENST00000409383,;SFTPB,intron_variant,,ENST00000428225,;SFTPB,intron_variant,,ENST00000494165,;SFTPB,intron_variant,,ENST00000519937,;SFTPB,intron_variant,,ENST00000491167,;SFTPB,downstream_gene_variant,,ENST00000473692,;,regulatory_region_variant,,ENSR00001183139,;	C	ENSG00000168878	ENST00000393822	Transcript	intron_variant						rs2118177	1		-1	SFTPB	HGNC	10801	protein_coding	YES	CCDS1983.2	ENSP00000377409		D6W5L6	UPI0000421A06					9/11		0.4888	0.8366	0.4409		0.3562	0.3668	0.3149					19017876,20233420,18550614,18776725,19951401,22662002					MODIFIER	1	SNV			1										1	.	CTT	.	.																					85890293
CCDC93	54520	.	GRCh37	2	118771566	118771566	+	Silent	SNP	C	A	A	rs11545372		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	A																c.6G>T	p.Gly2=	p.G2=	ENST00000376300	1/24	36	0	36	10			CCDC93,synonymous_variant,p.Gly2=,ENST00000376300,NM_019044.4;CCDC93,synonymous_variant,p.Gly2=,ENST00000319432,;RN7SL111P,upstream_gene_variant,,ENST00000468841,;AC009303.1,downstream_gene_variant,,ENST00000588042,;AC009303.1,downstream_gene_variant,,ENST00000590516,;,regulatory_region_variant,,ENSR00000122209,;	A	ENSG00000125633	ENST00000376300	Transcript	synonymous_variant	144/6899	6/1896	2/631	G	ggG/ggT	rs11545372	1		-1	CCDC93	HGNC	25611	protein_coding	YES	CCDS2121.2	ENSP00000365477	Q567U6		UPI0000207DEC	NM_019044.4			1/24		PANTHER:PTHR16441	0.3203	0.4894	0.2421		0.1409	0.3459	0.3057	0.4153	0.3296								LOW	1	SNV														.	ACC	.	.												0.2887	0.4202	0.1786	0.3729	0.1248	0.2214	0.3315	0.3169	0.3051	118771566
CCDC148	130940	.	GRCh37	2	159170495	159170495	+	Intron	SNP	T	T	G	rs751981170		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.765-89A>C			ENST00000283233		46			68			CCDC148,intron_variant,,ENST00000283233,NM_138803.3;CCDC148,intron_variant,,ENST00000409187,;CCDC148,intron_variant,,ENST00000536771,NM_001171637.1;CCDC148,intron_variant,,ENST00000417066,;CCDC148,intron_variant,,ENST00000448656,;CCDC148,intron_variant,,ENST00000451554,;CCDC148,intron_variant,,ENST00000454257,;,regulatory_region_variant,,ENSR00001629314,;	G	ENSG00000153237	ENST00000283233	Transcript	intron_variant						rs751981170	2		-1	CCDC148	HGNC	25191	protein_coding	YES	CCDS33304.1	ENSP00000283233	Q8NFR7		UPI0000208F63	NM_138803.3				7/13																		MODIFIER	1	SNV														.	GTA	.	.																					159170495
LRP2	4036	.	GRCh37	2	170070247	170070247	+	Missense_Mutation	SNP	T	T	G			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.5960A>C	p.Asp1987Ala	p.D1987A	ENST00000263816	36/79	191	169	22	150	150	0	LRP2,missense_variant,p.Asp1987Ala,ENST00000263816,NM_004525.2;	G	ENSG00000081479	ENST00000263816	Transcript	missense_variant	6246/15808	5960/13968	1987/4655	D/A	gAt/gCt	COSV55572497	1		-1	LRP2	HGNC	6694	protein_coding	YES	CCDS2232.1	ENSP00000263816	P98164	Q9NP34,Q53TL0,Q4ZG84	UPI0000141BA5	NM_004525.2	deleterious(0.02)	probably_damaging(0.997)	36/79		PROSITE_profiles:PS51120,PANTHER:PTHR10529,PANTHER:PTHR10529:SF220,Gene3D:2.120.10.30,SMART:SM00135,Superfamily:SSF63825											1						MODERATE	1	SNV			1										1	.	ATC	.	.																					170070247
STK11IP	114790	.	GRCh37	2	220479255	220479255	+	Silent	SNP	G	G	A	rs747326290		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.2889G>A	p.Ala963=	p.A963=	ENST00000295641	23/25	262	199	62	148	146	0	STK11IP,synonymous_variant,p.Ala952=,ENST00000456909,;STK11IP,synonymous_variant,p.Ala963=,ENST00000295641,NM_052902.2;STK11IP,synonymous_variant,p.Ala52=,ENST00000447191,;STK11IP,downstream_gene_variant,,ENST00000483319,;STK11IP,synonymous_variant,p.Ala145=,ENST00000413891,;STK11IP,non_coding_transcript_exon_variant,,ENST00000495941,;STK11IP,downstream_gene_variant,,ENST00000475396,;STK11IP,upstream_gene_variant,,ENST00000494777,;	A	ENSG00000144589	ENST00000295641	Transcript	synonymous_variant	2932/3601	2889/3300	963/1099	A	gcG/gcA	rs747326290,COSV55255283	1		1	STK11IP	HGNC	19184	protein_coding	YES	CCDS46521.1	ENSP00000295641	Q8N1F8	C9JQV3	UPI0001AE7798	NM_052902.2			23/25		PANTHER:PTHR15454:SF16,PANTHER:PTHR15454											0,1						LOW	1	SNV			0,1											.	CGT	.	.												8.047e-06						1.778e-05			220479255
ARMC9	80210	.	GRCh37	2	232121173	232121173	+	Intron	SNP	A	A	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.880-126A>C			ENST00000349938		120	115	5	114	111	1	ARMC9,intron_variant,,ENST00000349938,NM_025139.4,NM_001271466.1;ARMC9,intron_variant,,ENST00000436339,;ARMC9,upstream_gene_variant,,ENST00000424740,;ARMC9,intron_variant,,ENST00000483477,;ARMC9,upstream_gene_variant,,ENST00000467698,;AC018738.2,downstream_gene_variant,,ENST00000441378,;,regulatory_region_variant,,ENSR00000131799,;	C	ENSG00000135931	ENST00000349938	Transcript	intron_variant							1		1	ARMC9	HGNC	20730	protein_coding	YES	CCDS2484.1	ENSP00000258417	Q7Z3E5	C9JW07	UPI00001AE7AC	NM_025139.4,NM_001271466.1				9/20																		MODIFIER	1	SNV													1	.	CAA	.	.																					232121173
FAM132B	151176	.	GRCh37	2	239073046	239073046	+	Intron	SNP	C	T	T	rs6760421		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.887+45C>T			ENST00000546354		4	0	4	1			FAM132B,intron_variant,,ENST00000344233,;FAM132B,intron_variant,,ENST00000546354,;FAM132B,upstream_gene_variant,,ENST00000357303,;FAM132B,non_coding_transcript_exon_variant,,ENST00000486834,;FAM132B,intron_variant,,ENST00000473274,;FAM132B,intron_variant,,ENST00000479091,;FAM132B,intron_variant,,ENST00000481917,;	T	ENSG00000178752	ENST00000546354	Transcript	intron_variant						rs6760421	1		1	FAM132B	HGNC	26727	protein_coding	YES		ENSP00000442304	Q4G0M1		UPI0000F07B77					6/7		0.2542	0.1498	0.2594		0.2063	0.339	0.3538										MODIFIER	1	SNV														.	CCT	.	.												0.3086	0.1485	0.2931	0.2314	0.2048	0.3301	0.3327	0.2907	0.384	239073046
PRR21	643905	.	GRCh37	2	240982228	240982228	+	Missense_Mutation	SNP	C	T	T	rs10439373		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	T																c.172G>A	p.Gly58Ser	p.G58S	ENST00000408934	1/1	669	86	572	414			PRR21,missense_variant,p.Gly58Ser,ENST00000408934,NM_001080835.1;PRR21,missense_variant,p.Gly58Ser,ENST00000486799,;OR6B3,downstream_gene_variant,,ENST00000319423,NM_173351.1;	T	ENSG00000221961	ENST00000408934	Transcript	missense_variant	172/1170	172/1170	58/389	G/S	Ggc/Agc	rs10439373	1		-1	PRR21	HGNC	33866	protein_coding	YES	CCDS33417.1	ENSP00000386166	Q8WXC7		UPI0000071C18	NM_001080835.1	tolerated_low_confidence(0.45)	benign(0.045)	1/1				0.6157	0.4481		0.506	0.502	0.4847	0.6017	0.4301								MODERATE	1	SNV														.	CCG	.	.												0.4978	0.7592	0.3568	0.365	0.588	0.5031	0.5183	0.4897	0.4233	240982228
FANCD2	2177	.	GRCh37	3	10108898	10108898	+	Silent	SNP	A	A	G	rs77246387		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.2391A>G	p.Val797=	p.V797=	ENST00000287647	26/43	133	127	6	120	120	0	FANCD2,synonymous_variant,p.Val797=,ENST00000287647,NM_033084.3;FANCD2,synonymous_variant,p.Val797=,ENST00000419585,;FANCD2,synonymous_variant,p.Val797=,ENST00000383807,NM_001018115.1;FANCD2,synonymous_variant,p.Val797=,ENST00000383806,;FANCD2,intron_variant,,ENST00000470757,;FANCD2,synonymous_variant,p.Val297=,ENST00000421731,;FANCD2,non_coding_transcript_exon_variant,,ENST00000480909,;	G	ENSG00000144554	ENST00000287647	Transcript	synonymous_variant	2484/5219	2391/4416	797/1471	V	gtA/gtG	rs77246387	1		1	FANCD2	HGNC	3585	protein_coding	YES	CCDS2595.1	ENSP00000287647	Q9BXW9		UPI000006F678	NM_033084.3			26/43		PANTHER:PTHR32086,Pfam:PF14631																	LOW	1	SNV													1	.	TAA	.	.												0.001814	0.005465	0.0008921	0.001065	0.001207	0.001006	0.002244	0.00107	0.0009205	10108898
SH3BP5	9467	.	GRCh37	3	15345924	15345924	+	Intron	SNP	G	G	A	rs9828229		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.202-186C>T			ENST00000383791		6	2	4	5			SH3BP5,intron_variant,,ENST00000253688,;SH3BP5,intron_variant,,ENST00000383791,NM_004844.4;SH3BP5,intron_variant,,ENST00000408919,NM_001018009.3;SH3BP5,intron_variant,,ENST00000426925,;SH3BP5,intron_variant,,ENST00000459627,;SH3BP5,intron_variant,,ENST00000465894,;SH3BP5,intron_variant,,ENST00000412806,;SH3BP5,intron_variant,,ENST00000450625,;	A	ENSG00000131370	ENST00000383791	Transcript	intron_variant						rs9828229	1		-1	SH3BP5	HGNC	10827	protein_coding	YES	CCDS2625.2	ENSP00000373301	O60239	Q6MZG3,C9JNW0,C9JK30,B2R7Y8	UPI00004C3DB7	NM_004844.4				2/8		0.4133	0.3623	0.3573		0.5972	0.34	0.408										MODIFIER	1	SNV														.	CGT	.	.																					15345924
GORASP1	64689	.	GRCh37	3	39145186	39145186	+	Intron	SNP	G	G	A	rs7629643		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.64-142C>T			ENST00000319283		8	3	5	8			GORASP1,intron_variant,,ENST00000319283,NM_031899.3;GORASP1,intron_variant,,ENST00000411813,;GORASP1,intron_variant,,ENST00000416741,;GORASP1,intron_variant,,ENST00000422110,NM_001278790.1;GORASP1,intron_variant,,ENST00000427459,;GORASP1,intron_variant,,ENST00000437458,;GORASP1,intron_variant,,ENST00000441081,;GORASP1,intron_variant,,ENST00000479927,NM_001278789.1;TTC21A,upstream_gene_variant,,ENST00000301819,NM_145755.2;TTC21A,upstream_gene_variant,,ENST00000431162,;TTC21A,upstream_gene_variant,,ENST00000440121,NM_001105513.2;GORASP1,non_coding_transcript_exon_variant,,ENST00000486133,;GORASP1,intron_variant,,ENST00000493751,;GORASP1,intron_variant,,ENST00000493938,;GORASP1,upstream_gene_variant,,ENST00000476334,;GORASP1,upstream_gene_variant,,ENST00000479124,;GORASP1,upstream_gene_variant,,ENST00000489587,;GORASP1,intron_variant,,ENST00000413243,;GORASP1,intron_variant,,ENST00000431601,;GORASP1,intron_variant,,ENST00000441302,;GORASP1,intron_variant,,ENST00000452389,;GORASP1,intron_variant,,ENST00000453680,;GORASP1,intron_variant,,ENST00000466443,;GORASP1,intron_variant,,ENST00000469471,;GORASP1,intron_variant,,ENST00000470910,;GORASP1,intron_variant,,ENST00000473827,;GORASP1,intron_variant,,ENST00000488479,;GORASP1,intron_variant,,ENST00000492064,;GORASP1,intron_variant,,ENST00000493851,;GORASP1,upstream_gene_variant,,ENST00000419156,;TTC21A,upstream_gene_variant,,ENST00000425163,;TTC21A,upstream_gene_variant,,ENST00000430597,;TTC21A,upstream_gene_variant,,ENST00000431559,;TTC21A,upstream_gene_variant,,ENST00000459702,;TTC21A,upstream_gene_variant,,ENST00000479954,;TTC21A,upstream_gene_variant,,ENST00000490036,;TTC21A,upstream_gene_variant,,ENST00000493337,;	A	ENSG00000114745	ENST00000319283	Transcript	intron_variant						rs7629643	1		-1	GORASP1	HGNC	16769	protein_coding	YES	CCDS2681.1	ENSP00000313869	Q9BQQ3	F8WD30,C9J5S6	UPI000007074D	NM_031899.3				1/8		0.4099	0.8858	0.2997		0.2986	0.2197	0.1554					30595370					MODIFIER	1	SNV			1											.	AGG	.	.																					39145186
NKTR	4820	.	GRCh37	3	42687278	42687278	+	Intron	SNP	C	C	T	rs73085333		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.4302-102C>T			ENST00000232978		28	18	10	12			NKTR,intron_variant,,ENST00000232978,NM_005385.3;RP4-613B23.1,intron_variant,,ENST00000434363,;RP4-613B23.1,intron_variant,,ENST00000438017,;RP4-613B23.1,intron_variant,,ENST00000445452,;NKTR,intron_variant,,ENST00000429888,;NKTR,intron_variant,,ENST00000490189,;	T	ENSG00000114857	ENST00000232978	Transcript	intron_variant						rs73085333	1		1	NKTR	HGNC	7833	protein_coding	YES	CCDS2702.1	ENSP00000232978	P30414		UPI00001301FD	NM_005385.3				16/16		0.2570	0.115	0.4856		0.1687	0.3777	0.2536										MODIFIER	1	SNV														.	ACT	.	.																					42687278
PRICKLE2	166336	.	GRCh37	3	64084857	64084857	+	Missense_Mutation	SNP	C	C	A			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.2405G>T	p.Arg802Leu	p.R802L	ENST00000295902	8/8	125	118	6	92	92	0	PRICKLE2,missense_variant,p.Arg802Leu,ENST00000295902,NM_198859.3;PRICKLE2,missense_variant,p.Arg858Leu,ENST00000564377,;RP11-129B22.1,non_coding_transcript_exon_variant,,ENST00000482609,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000460946,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000476308,;PRICKLE2-AS2,upstream_gene_variant,,ENST00000484703,;	A	ENSG00000163637	ENST00000295902	Transcript	missense_variant	2991/8305	2405/2535	802/844	R/L	cGa/cTa	COSV55772247	1		-1	PRICKLE2	HGNC	20340	protein_coding	YES	CCDS2902.1	ENSP00000295902	Q7Z3G6	C9JY03	UPI0000160A8B	NM_198859.3	deleterious(0.02)	benign(0.195)	8/8		PANTHER:PTHR24218:SF5,PANTHER:PTHR24218											1						MODERATE	1	SNV			1										1	.	TCG	.	.																					64084857
MYH15	22989	.	GRCh37	3	108229122	108229122	+	Intron	SNP	C	G	G	rs3843872		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.148+168G>C			ENST00000273353		5	0	5	6			MYH15,intron_variant,,ENST00000273353,NM_014981.1;	G	ENSG00000144821	ENST00000273353	Transcript	intron_variant						rs3843872	1		-1	MYH15	HGNC	31073	protein_coding	YES	CCDS43127.1	ENSP00000273353	Q9Y2K3	H9XFA0	UPI0000253B6F	NM_014981.1				2/41		0.1538	0.093	0.1945		0.0139	0.3191	0.181					18360741					MODIFIER	1	SNV														.	CCC	.	.																					108229122
PPP2R3A	5523	.	GRCh37	3	135820792	135820792	+	Intron	SNP	C	C	A	rs1165013938		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.2928-57C>A			ENST00000264977		78	45	33	85	78	7	PPP2R3A,intron_variant,,ENST00000264977,NM_001190447.1,NM_002718.4;PPP2R3A,intron_variant,,ENST00000334546,NM_181897.2;PPP2R3A,intron_variant,,ENST00000490467,;PPP2R3A,upstream_gene_variant,,ENST00000469270,;	A	ENSG00000073711	ENST00000264977	Transcript	intron_variant						rs1165013938	1		1	PPP2R3A	HGNC	9307	protein_coding	YES	CCDS3087.1	ENSP00000264977	Q06190		UPI0000124EAC	NM_001190447.1,NM_002718.4				10/13																		MODIFIER	1	SNV														.	TCT	.	.																					135820792
PLSCR1	5359	.	GRCh37	3	146243308	146243308	+	Intron	SNP	G	G	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.355+84C>T			ENST00000342435		45	28	17	50	49	0	PLSCR1,intron_variant,,ENST00000342435,NM_021105.2;PLSCR1,intron_variant,,ENST00000448205,;PLSCR1,intron_variant,,ENST00000448787,;PLSCR1,intron_variant,,ENST00000462666,;PLSCR1,intron_variant,,ENST00000472349,;PLSCR1,intron_variant,,ENST00000483300,;PLSCR1,intron_variant,,ENST00000486631,;PLSCR1,intron_variant,,ENST00000487389,;PLSCR1,upstream_gene_variant,,ENST00000470496,;PLSCR1,intron_variant,,ENST00000463777,;PLSCR1,intron_variant,,ENST00000468985,;PLSCR1,intron_variant,,ENST00000478267,;PLSCR1,intron_variant,,ENST00000488253,;PLSCR1,intron_variant,,ENST00000489775,;PLSCR1,intron_variant,,ENST00000493432,;PLSCR1,intron_variant,,ENST00000494568,;PLSCR1,downstream_gene_variant,,ENST00000469266,;PLSCR1,downstream_gene_variant,,ENST00000490745,;	A	ENSG00000188313	ENST00000342435	Transcript	intron_variant							1		-1	PLSCR1	HGNC	9092	protein_coding	YES	CCDS3135.1	ENSP00000345494	O15162	C9JSI9,C9JE06,C9J7K9	UPI0000001627	NM_021105.2				5/8																		MODIFIER	1	SNV														.	TGT	.	.																					146243308
LPP	4026	.	GRCh37	3	188478225	188478225	+	Intron	SNP	C	C	T	rs55675647		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1410+155C>T			ENST00000312675		16	12	4	23	22	0	LPP,intron_variant,,ENST00000312675,NM_005578.3,NM_001167672.1;LPP,intron_variant,,ENST00000543006,NM_001167671.1,NM_001167672.1;LPP,intron_variant,,ENST00000459897,;LPP,downstream_gene_variant,,ENST00000471917,;,regulatory_region_variant,,ENSR00001671486,;	T	ENSG00000145012	ENST00000312675	Transcript	intron_variant						rs55675647	1		1	LPP	HGNC	6679	protein_coding	YES	CCDS3291.1	ENSP00000318089	Q93052	C9JT42,C9JIY7,C9JE51,C9J5C8,C9J4E3,C9J3U9,C9J2R5,C9J1K7,B7Z871	UPI000002E034	NM_005578.3,NM_001167672.1				8/10																		MODIFIER	1	SNV													1	.	GCG	.	.																					188478225
ATP13A4	84239	.	GRCh37	3	193177124	193177124	+	Intron	SNP	T	T	C	rs116583678		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1524-104A>G			ENST00000342695		6	2	4	6			ATP13A4,intron_variant,,ENST00000295548,;ATP13A4,intron_variant,,ENST00000342695,NM_032279.2;ATP13A4,intron_variant,,ENST00000392443,;ATP13A4,intron_variant,,ENST00000428352,;ATP13A4,intron_variant,,ENST00000450950,;ATP13A4,intron_variant,,ENST00000490925,;	C	ENSG00000127249	ENST00000342695	Transcript	intron_variant						rs116583678	1		-1	ATP13A4	HGNC	25422	protein_coding	YES	CCDS3304.2	ENSP00000339182	Q4VNC1		UPI0000520D50	NM_032279.2				13/29		0.0016		0.0043			0.003	0.002										MODIFIER	1	SNV														.	TTT	.	.																					193177124
TMEM175	84286	.	GRCh37	4	952210	952210	+	Missense_Mutation	SNP	C	T	T	rs201314478		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1441C>T	p.Arg481Trp	p.R481W	ENST00000264771	11/11	17	1	16	2	2	0	TMEM175,missense_variant,p.Arg481Trp,ENST00000264771,NM_032326.2;TMEM175,missense_variant,p.Arg365Trp,ENST00000515740,;TMEM175,missense_variant,p.Arg399Trp,ENST00000508204,;DGKQ,downstream_gene_variant,,ENST00000273814,NM_001347.3;DGKQ,downstream_gene_variant,,ENST00000509465,;TMEM175,downstream_gene_variant,,ENST00000509508,;TMEM175,downstream_gene_variant,,ENST00000510493,;DGKQ,downstream_gene_variant,,ENST00000515182,;TMEM175,downstream_gene_variant,,ENST00000515492,;DGKQ,downstream_gene_variant,,ENST00000502309,;TMEM175,3_prime_UTR_variant,,ENST00000513952,;TMEM175,non_coding_transcript_exon_variant,,ENST00000438836,;TMEM175,downstream_gene_variant,,ENST00000452360,;TMEM175,downstream_gene_variant,,ENST00000506669,;TMEM175,downstream_gene_variant,,ENST00000515876,;	T	ENSG00000127419	ENST00000264771	Transcript	missense_variant	1626/1860	1441/1515	481/504	R/W	Cgg/Tgg	rs201314478	1		1	TMEM175	HGNC	28709	protein_coding	YES	CCDS3341.1	ENSP00000264771	Q9BSA9	E7ETE6,D6RIZ2,D6RBE5,D3DVN5	UPI000006D921	NM_032326.2	tolerated(0.06)	benign(0)	11/11		PANTHER:PTHR31462,PANTHER:PTHR31462:SF2,Low_complexity_(Seg):seg	0.0004		0.0029														MODERATE	1	SNV														.	CCG	.	.												0.001987	0.000453	0.003133	0.002463	0.0004639		0.00279	0.003091	0.0001338	952210
CPEB2	132864	.	GRCh37	4	15067943	15067943	+	Missense_Mutation	SNP	A	A	G			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.3044A>G	p.His1015Arg	p.H1015R	ENST00000538197	12/12	209	161	48	194	191	0	CPEB2,missense_variant,p.His1015Arg,ENST00000538197,NM_001177382.1;CPEB2,missense_variant,p.His1007Arg,ENST00000541112,NM_182485.2;CPEB2,missense_variant,p.His988Arg,ENST00000442003,NM_001177381.1,NM_001177383.1;CPEB2,missense_variant,p.His578Arg,ENST00000259997,;CPEB2,missense_variant,p.His548Arg,ENST00000382395,;CPEB2,missense_variant,p.His543Arg,ENST00000382401,NM_001177384.1,NM_182646.2;CPEB2,missense_variant,p.His570Arg,ENST00000507071,;CPEB2,missense_variant,p.His540Arg,ENST00000345451,;CPEB2,downstream_gene_variant,,ENST00000509684,;RP11-665G4.1,non_coding_transcript_exon_variant,,ENST00000513384,;RP11-665G4.1,intron_variant,,ENST00000502344,;	G	ENSG00000137449	ENST00000538197	Transcript	missense_variant	3044/6878	3044/3105	1015/1034	H/R	cAt/cGt	COSV52595335	1		1	CPEB2	HGNC	21745	protein_coding	YES	CCDS56325.1	ENSP00000443985		J3KN18,H0Y9D9,F5H160	UPI0001D0434B	NM_001177382.1	deleterious_low_confidence(0)	probably_damaging(1)	12/12		PANTHER:PTHR12566											1						MODERATE	1	SNV			1											.	CAT	.	.																					15067943
LGI2	55203	.	GRCh37	4	25032135	25032135	+	Missense_Mutation	SNP	C	C	T	rs74901868		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.181G>A	p.Gly61Ser	p.G61S	ENST00000382114	1/8	22	11	11	6			LGI2,missense_variant,p.Gly61Ser,ENST00000382114,NM_018176.3;LGI2,missense_variant,p.Gly52Ser,ENST00000512108,;,regulatory_region_variant,,ENSR00000166862,;,regulatory_region_variant,,ENSR00001675262,;	T	ENSG00000153012	ENST00000382114	Transcript	missense_variant	367/6428	181/1638	61/545	G/S	Ggc/Agc	rs74901868	1		-1	LGI2	HGNC	18710	protein_coding	YES	CCDS3431.1	ENSP00000371548	Q8N0V4		UPI0000047256	NM_018176.3	tolerated(0.29)	benign(0.003)	1/8		PANTHER:PTHR24367:SF21,PANTHER:PTHR24367	0.1799	0.1611	0.2133		0.2262	0.1879	0.1258	0.158	0.1966								MODERATE	1	SNV														.	CCC	.	.												0.1843	0.1533	0.2319	0.2319	0.246	0.1227	0.1775	0.1995	0.1541	25032135
CNOT6L	246175	.	GRCh37	4	78677973	78677973	+	Intron	SNP	A	A	G	rs947678252		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.490+43T>C			ENST00000264903		148	99	49	117	116	1	CNOT6L,intron_variant,,ENST00000264903,NM_144571.2;CNOT6L,intron_variant,,ENST00000504123,NM_001286790.1;CNOT6L,intron_variant,,ENST00000512485,;CNOT6L,intron_variant,,ENST00000515506,;CNOT6L,downstream_gene_variant,,ENST00000515441,;CNOT6L,intron_variant,,ENST00000506166,;CNOT6L,intron_variant,,ENST00000504804,;	G	ENSG00000138767	ENST00000264903	Transcript	intron_variant						rs947678252	1		-1	CNOT6L	HGNC	18042	protein_coding	YES	CCDS47082.1	ENSP00000264903	Q96LI5	D6RGK9	UPI0000E445DF	NM_144571.2				5/11																		MODIFIER	1	SNV														.	AAT	.	.												1.084e-05						2.51e-05			78677973
METTL14	57721	.	GRCh37	4	119609200	119609200	+	Intron	SNP	G	G	T	rs77393270		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.155+34G>T			ENST00000388822		58	53	4	68	68	0	METTL14,intron_variant,,ENST00000388822,;METTL14,intron_variant,,ENST00000506780,NM_020961.2;METTL14,intron_variant,,ENST00000508801,;METTL14,upstream_gene_variant,,ENST00000502564,;	T	ENSG00000145388	ENST00000388822	Transcript	intron_variant						rs77393270	1		1	METTL14	HGNC	29330	protein_coding	YES	CCDS34053.1	ENSP00000373474	Q9HCE5	B4DJF7	UPI00000437DD					2/10																		MODIFIER	1	SNV														.	TGA	.	.																					119609200
LRBA	987	.	GRCh37	4	151821369	151821369	+	Missense_Mutation	SNP	C	C	A	rs762914566		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1756G>T	p.Val586Phe	p.V586F	ENST00000357115	14/58	88	68	20	92	91	0	LRBA,missense_variant,p.Val586Phe,ENST00000535741,;LRBA,missense_variant,p.Val586Phe,ENST00000510413,NM_001199282.2;LRBA,missense_variant,p.Val586Phe,ENST00000357115,NM_006726.4;LRBA,missense_variant,p.Val586Phe,ENST00000507224,;	A	ENSG00000198589	ENST00000357115	Transcript	missense_variant,splice_region_variant	2000/9899	1756/8592	586/2863	V/F	Gtt/Ttt	rs762914566,COSV63964098	1		-1	LRBA	HGNC	1742	protein_coding	YES	CCDS3773.1	ENSP00000349629	P50851	Q7KZN3	UPI000013E35C	NM_006726.4	deleterious(0)	probably_damaging(0.96)	14/58		PANTHER:PTHR13743,PANTHER:PTHR13743:SF64											0,1						MODERATE	1	SNV			0,1										1	.	ACC	.	.												4.086e-06	6.226e-05								151821369
ZDHHC11	79844	.	GRCh37	5	848578	848578	+	Intron	SNP	G	G	A	rs570508705		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.401+19C>T			ENST00000283441		14	7	7	18	18	0	ZDHHC11,intron_variant,,ENST00000283441,NM_024786.2;ZDHHC11,intron_variant,,ENST00000424784,;ZDHHC11,intron_variant,,ENST00000511193,;ZDHHC11,upstream_gene_variant,,ENST00000511539,;ZDHHC11,intron_variant,,ENST00000508951,;ZDHHC11,intron_variant,,ENST00000512775,;BRD9,downstream_gene_variant,,ENST00000493082,;ZDHHC11,upstream_gene_variant,,ENST00000503880,;ZDHHC11,upstream_gene_variant,,ENST00000505815,;ZDHHC11,upstream_gene_variant,,ENST00000507800,;ZDHHC11,upstream_gene_variant,,ENST00000512190,;	A	ENSG00000188818	ENST00000283441	Transcript	intron_variant						rs570508705	1		-1	ZDHHC11	HGNC	19158	protein_coding	YES	CCDS3857.1	ENSP00000283441	Q9H8X9		UPI000013C384	NM_024786.2				2/12		0.1300	0.1188	0.1354		0.1161	0.16	0.1247										MODIFIER	1	SNV														.	CGG	.	.												0.09449	0.1431	0.09472	0.152	0.04753	0.1613	0.07879	0.07492	0.09446	848578
CTD-2324F15.2	401172	.	GRCh37	5	6312879	6312879	+	Intron	SNP	C	C	G	rs2168655		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																n.144-50G>C			ENST00000507444		59	38	21	20			CTD-2324F15.2,intron_variant,,ENST00000507444,;	G	ENSG00000250490	ENST00000507444	Transcript	intron_variant,non_coding_transcript_variant						rs2168655	1		-1	CTD-2324F15.2	Clone_based_vega_gene		lincRNA	YES										1/1																		MODIFIER	1	SNV														.	ACA	.	.												0.3326	0.326	0.3786	0.2306	0.3542	0.2768	0.3251	0.3227	0.3118	6312879
DNAH5	1767	.	GRCh37	5	13810149	13810149	+	Intron	SNP	G	A	A	rs35732567		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.7609+19C>T			ENST00000265104		12	3	9	3			DNAH5,intron_variant,,ENST00000265104,NM_001369.2;DNAH5,intron_variant,,ENST00000512443,;	A	ENSG00000039139	ENST00000265104	Transcript	intron_variant						rs35732567	1		-1	DNAH5	HGNC	2950	protein_coding	YES	CCDS3882.1	ENSP00000265104	Q8TE73	O95496	UPI0000110101	NM_001369.2				45/78		0.4067	0.2943	0.4092		0.6379	0.3976	0.3282	0.3174	0.3661	benign		25741868					MODIFIER	1	SNV			1										1	.	GGA	.	.												0.3929	0.3233	0.3992	0.3564	0.646	0.3621	0.3843	0.4061	0.3392	13810149
AGGF1	55109	.	GRCh37	5	76349716	76349716	+	Intron	SNP	A	A	C	rs200634999		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1468-74A>C			ENST00000312916		51	16	35	37	34	3	AGGF1,intron_variant,,ENST00000312916,NM_018046.4;	C	ENSG00000164252	ENST00000312916	Transcript	intron_variant						rs200634999	1		1	AGGF1	HGNC	24684	protein_coding	YES	CCDS4035.1	ENSP00000316109	Q8N302	A8K029	UPI0000231C8D	NM_018046.4				9/13																		MODIFIER	1	SNV													1	.	CAT	.	.																					76349716
MCC	4163	.	GRCh37	5	112364613	112364613	+	Intron	SNP	G	G	A	rs918537542		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.2879+18C>T			ENST00000408903		159	120	39	158	157	0	MCC,intron_variant,,ENST00000302475,NM_002387.2;MCC,intron_variant,,ENST00000408903,NM_001085377.1;MCC,intron_variant,,ENST00000515367,;MCC,non_coding_transcript_exon_variant,,ENST00000514701,;	A	ENSG00000171444	ENST00000408903	Transcript	intron_variant						rs918537542	1		-1	MCC	HGNC	6935	protein_coding	YES	CCDS43351.1	ENSP00000386227	P23508	D6REY2	UPI00015E06EA	NM_001085377.1				18/18																		MODIFIER	1	SNV														.	GGT	.	.																					112364613
ACSL6	23305	.	GRCh37	5	131320961	131320961	+	Intron	SNP	C	C	G	rs115222986		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.916+139G>C			ENST00000379264		26	13	13	11			ACSL6,intron_variant,,ENST00000296869,NM_015256.3,NM_001205247.1;ACSL6,intron_variant,,ENST00000357096,;ACSL6,intron_variant,,ENST00000379240,;ACSL6,intron_variant,,ENST00000379244,;ACSL6,intron_variant,,ENST00000379246,NM_001205250.1;ACSL6,intron_variant,,ENST00000379249,;ACSL6,intron_variant,,ENST00000379255,NM_001205251.1;ACSL6,intron_variant,,ENST00000379264,NM_001009185.2;ACSL6,intron_variant,,ENST00000379272,;ACSL6,intron_variant,,ENST00000431707,;ACSL6,intron_variant,,ENST00000434099,;ACSL6,intron_variant,,ENST00000543479,NM_001205248.1;ACSL6,intron_variant,,ENST00000544770,;ACSL6,downstream_gene_variant,,ENST00000414078,;ACSL6,downstream_gene_variant,,ENST00000416557,;ACSL6,downstream_gene_variant,,ENST00000419502,;ACSL6,downstream_gene_variant,,ENST00000430403,;ACSL6,downstream_gene_variant,,ENST00000441995,;ACSL6,non_coding_transcript_exon_variant,,ENST00000489047,;ACSL6,intron_variant,,ENST00000413683,;	G	ENSG00000164398	ENST00000379264	Transcript	intron_variant						rs115222986,COSV57294202	1		-1	ACSL6	HGNC	16496	protein_coding	YES	CCDS34229.1	ENSP00000368566	Q9UKU0	G3V1S9,C9JPA5,C9JK59,C9J4I1,C9J3Z0,B3KV64	UPI00004BA928	NM_001009185.2				9/20		0.4551	0.6921	0.4006		0.5258	0.2624	0.2986				0,1						MODIFIER	1	SNV			0,1										1	.	TCA	.	.																					131320961
HLA-C	3107	.	GRCh37	6	31238992	31238992	+	Silent	SNP	G	G	C	rs41550715		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.477C>G	p.Ala159=	p.A159=	ENST00000376228	3/8	25	11	14	5			HLA-C,synonymous_variant,p.Ala159=,ENST00000383329,;HLA-C,synonymous_variant,p.Ala159=,ENST00000376228,NM_002117.5;HLA-C,synonymous_variant,p.Ala159=,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,non_coding_transcript_exon_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,;HLA-C,upstream_gene_variant,,ENST00000470363,;USP8P1,upstream_gene_variant,,ENST00000494673,;,regulatory_region_variant,,ENSR00000195522,;	C	ENSG00000204525	ENST00000376228	Transcript	synonymous_variant	492/1536	477/1101	159/366	A	gcC/gcG	rs41550715	1		-1	HLA-C	HGNC	4933	protein_coding	YES	CCDS34393.1	ENSP00000365402	P10321	S5DU09,S5DN70,S5DLG2,S5DLF2,S5DI32,S5DI31,S5DHQ8,S5DHQ4,Q6R739,N0A4B4,M9XMB2,M9PAK8,M9PAK7,M9PAG6,M9PAG3,M9PAG2,M9PAF9,M9PAF5,M9PAF4,M9PAF2,M9PAC6,M9PA33,M9P9W6,M9P9W3,M9P9V5,M9P9U9,M9P9U4,M9P9R9,M9P9P5,M9P9N1,M9P9M9,M9P9L6,M9P9L0,M9P9H8,M9P9H2,M9P9F8,M9P9F2,M9P9D8,M9P9A7,M9P971,M9P965,M9P962,M9P961,M9P959,M9P955,M9P944,M9P8M1,M9P8L9,M9P8L8,M9P8L7,M9P8L4,M9P8L2,M9P8L0,M9P8K5,Q9TNT2,Q9MY32,Q95HC2,Q8HWM5,Q8HWG1,Q5C9P9,Q29752,Q0MT77,O19579,K9L8F4,K9L7Z3,K9L7R8,K9L7R5,K9L7E8,J9PVP1,J9PVD3,J9PVC3,J7K040,J7JWN4,J7JHR0,I7APJ0,I7A4F1,I6TRY5,I6TRX6,I6TN19,I6TF01,I6SJ94,I6NXM6,I6NXH6,I6NS49,I6NN86,I6MHJ6,I6M570,I6M569,I2GUK7,H9BQ96,H9BQ94,H6V083,H6A2G1,H2DMK4,H2DMJ8,H2BE96,G9I2P1,G9I2N8,G9I2N5,G9I2N2,G9HWA9,G9HWA8,G9HW96,G9HW51,G3D6H6,G3D6G8,G3D6F7,G3D6F5,G3D6E6,G1EQI7,G1EQI3,G1EQH0,G1EQD5,G1EQ80,G1EQ55,G1ENX7,G1ENX4,G1ENX1,G1ENW1,G1ENW0,G1ENV4,G1ENV3,G1ENV2,G1ENT9,G1ENT7,G1ENT3,G1ENT1,G1ENT0,G1EMU8,G1EMU5,G1EMT8,G1EMT7,G1EMT3,G1EMT2,G1EMS4,G1EMS2,G1EMR7,G1EMR6,G1EMR4,G1EMR0,G1EMQ7,G0ZMM1,G0ZMJ9,G0X8S7,G0WVC4,F8SY67,F8SL02,F8SL01,F8SKZ7,F8SKZ5,F8SKZ4,F8SKY8,F8R8K2,F8R1B3,F6KVT8,F6KS12,F6KS10,F6KS09,F6KS07,F6KRY5,F6KRY2,F6KRY0,F6KRX9,F6KRX3,F6KRW4,F6KRW3,F6IQL8,F6IQL6,F6IQL4,F6IQL2,F6IQK7,F6IQK5,F6IQK4,F6IQK3,F6IQK2,F6IQK1,F6IQJ9,F4YU88,F4YU76,F2VNS0,F2VNR5,F2VNQ5,F2VNQ1,F1CCL2,F1CCK3,F1CCJ3,E3SWK0,E3SGA8,E3SGA7,E3SGA4,E3Q1I6,E2GJI9,E2GJH5,E2DHB8,E1Y7F7,E1U661,E0YTP0,E0YTN9,E0X9L4,E0WBV9,E0WBV8,D9UAZ7,D7RJ45,D7NQZ6,D7NP34,D6MLE9,D6MLD2,D6ML93,D6MKV1,D6MJJ2,D6MJI1,D6MJH9,D6C6F9,D6C6D5,D6C6D4,D6C6C3,D5M8B1,D5FZR1,D5FZM4,D3U749,D3U748,D3U733,D3U3P8,D3U3P6,D2DKH1,C9WEV2,C9WEV1,C9WEU1,C9WES3,C9WER9,C9WER5,C9WER2,C8CHA9,C8CH96,C7FDU3,C7FDU2,C7FDT6,C7EDP3,C7C4Z5,C6K4P2,C6K4N9,C6K4N7,C6K4M5,C6JSX9,C5J031,C5IZU8,C5IZU6,C0KJZ4,B9WPN5,B8Y6A8,B5BLP2,B1PQ27,B0JF23	UPI000008AEBB	NM_002117.5			3/8		PANTHER:PTHR16675:SF157,PANTHER:PTHR16675,Gene3D:3.30.500.10,Pfam:PF00129,Superfamily:SSF54452	0.4050	0.4607	0.4207		0.3621	0.3986	0.3691										LOW	1	SNV													1	.	CGG	.	.												0.3459	0.4079	0.3841	0.479	0.2573	0.3436	0.3263	0.329	0.3476	31238992
SYNGAP1	8831	.	GRCh37	6	33415553	33415553	+	Intron	SNP	A	A	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.3795-67A>G			ENST00000418600		25	19	6	25	25	0	SYNGAP1,intron_variant,,ENST00000293748,;SYNGAP1,intron_variant,,ENST00000418600,NM_006772.2;SYNGAP1,intron_variant,,ENST00000428982,;SYNGAP1,intron_variant,,ENST00000449372,;SYNGAP1,intron_variant,,ENST00000486399,;SYNGAP1,intron_variant,,ENST00000496374,;SYNGAP1,intron_variant,,ENST00000470232,;	G	ENSG00000197283	ENST00000418600	Transcript	intron_variant							1		1	SYNGAP1	HGNC	11497	protein_coding	YES	CCDS34434.2	ENSP00000403636	Q96PV0		UPI0000470C44	NM_006772.2				17/18																		MODIFIER	1	SNV													1	.	TAT	.	.																					33415553
PGC	5225	.	GRCh37	6	41712443	41712443	+	Missense_Mutation	SNP	G	G	A	rs151306066		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.163C>T	p.Arg55Cys	p.R55C	ENST00000373025	2/9	117	84	33	64	64	0	PGC,missense_variant,p.Arg55Cys,ENST00000373025,NM_002630.3;PGC,missense_variant,p.Arg55Cys,ENST00000425343,NM_001166424.1;PGC,missense_variant,p.Arg55Cys,ENST00000356667,;PGC,missense_variant,p.Arg59Cys,ENST00000415707,;	A	ENSG00000096088	ENST00000373025	Transcript	missense_variant	226/1371	163/1167	55/388	R/C	Cgc/Tgc	rs151306066,COSV63124005	1		-1	PGC	HGNC	8890	protein_coding	YES	CCDS4859.1	ENSP00000362116	P20142		UPI00001315CC	NM_002630.3	tolerated(0.15)	benign(0.28)	2/9		PANTHER:PTHR13683,PANTHER:PTHR13683:SF242,Superfamily:SSF50630	0.0002		0.0014						0.0003488		0,1						MODERATE	1	SNV			0,1											.	CGG	.	.												2.784e-05						5.276e-05		3.267e-05	41712443
TMEM63B	55362	.	GRCh37	6	44114773	44114773	+	Intron	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.863+109G>T			ENST00000259746		20	14	6	27	27	0	TMEM63B,intron_variant,,ENST00000259746,;TMEM63B,intron_variant,,ENST00000323267,NM_018426.1;TMEM63B,intron_variant,,ENST00000371893,;TMEM63B,intron_variant,,ENST00000497371,;TMEM63B,intron_variant,,ENST00000525873,;TMEM63B,intron_variant,,ENST00000533121,;TMEM63B,intron_variant,,ENST00000534326,;	T	ENSG00000137216	ENST00000259746	Transcript	intron_variant							1		1	TMEM63B	HGNC	17735	protein_coding	YES	CCDS34461.1	ENSP00000259746	Q5T3F8	E9PNG1	UPI000020DDEE					11/23																		MODIFIER	1	SNV														.	TGA	.	.																					44114773
PKHD1	5314	.	GRCh37	6	51612753	51612753	+	Missense_Mutation	SNP	G	G	T	rs1248397819		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.9661C>A	p.Pro3221Thr	p.P3221T	ENST00000371117	58/67	143	138	5	94	94	0	PKHD1,missense_variant,p.Pro3221Thr,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Pro3221Thr,ENST00000340994,NM_170724.2;	T	ENSG00000170927	ENST00000371117	Transcript	missense_variant	9937/16282	9661/12225	3221/4074	P/T	Ccg/Acg	rs1248397819	1		-1	PKHD1	HGNC	9016	protein_coding	YES	CCDS4935.1	ENSP00000360158	P08F94		UPI000013C4C0	NM_138694.3	deleterious(0.01)	probably_damaging(0.997)	58/67		PANTHER:PTHR11915,PANTHER:PTHR11915:SF230																	MODERATE	1	SNV													1	.	GGC	.	.																					51612753
BMP5	653	.	GRCh37	6	55623942	55623942	+	Intron	SNP	C	C	A	rs779462976		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1105-29G>T			ENST00000370830		19	15	4	17	17	0	BMP5,intron_variant,,ENST00000370830,NM_021073.2;BMP5,intron_variant,,ENST00000446683,;,regulatory_region_variant,,ENSR00001364485,;	A	ENSG00000112175	ENST00000370830	Transcript	intron_variant						rs779462976,COSV63702700,COSV63706939	1		-1	BMP5	HGNC	1072	protein_coding	YES	CCDS4958.1	ENSP00000359866	P22003	M9VUD0	UPI0000126A2C	NM_021073.2				5/6												0,1,1						MODIFIER	1	SNV			0,1,1										1	.	ACA	.	.																					55623942
COL12A1	1303	.	GRCh37	6	75864107	75864107	+	Intron	SNP	C	C	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.3565+25G>A			ENST00000322507		157	123	34	130	130	0	COL12A1,intron_variant,,ENST00000322507,NM_004370.5;COL12A1,intron_variant,,ENST00000345356,NM_080645.2;COL12A1,intron_variant,,ENST00000416123,;COL12A1,intron_variant,,ENST00000483888,;COL12A1,upstream_gene_variant,,ENST00000419671,;	T	ENSG00000111799	ENST00000322507	Transcript	intron_variant							1		-1	COL12A1	HGNC	2188	protein_coding	YES	CCDS43482.1	ENSP00000325146	Q99715		UPI000045890B	NM_004370.5				17/65																		MODIFIER	1	SNV													1	.	TCA	.	.																					75864107
SYNE1	23345	.	GRCh37	6	152763259	152763259	+	Missense_Mutation	SNP	G	G	A			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.3959C>T	p.Thr1320Ile	p.T1320I	ENST00000367255	31/146	92	72	20	40	39	0	SYNE1,missense_variant,p.Thr1320Ile,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Thr1320Ile,ENST00000265368,;SYNE1,missense_variant,p.Thr1327Ile,ENST00000448038,;SYNE1,missense_variant,p.Thr1327Ile,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Thr1386Ile,ENST00000341594,;SYNE1,missense_variant,p.Thr1310Ile,ENST00000367248,;SYNE1,missense_variant,p.Thr1320Ile,ENST00000367253,;SYNE1,missense_variant,p.Thr1320Ile,ENST00000413186,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,;	A	ENSG00000131018	ENST00000367255	Transcript	missense_variant	4561/27748	3959/26394	1320/8797	T/I	aCa/aTa	COSV55092793	1		-1	SYNE1	HGNC	17089	protein_coding	YES	CCDS5236.2	ENSP00000356224	Q8NF91		UPI000204AF58	NM_182961.3	deleterious_low_confidence(0.01)	benign(0.367)	31/146		Coiled-coils_(Ncoils):Coil,PANTHER:PTHR11915,PANTHER:PTHR11915:SF267											1						MODERATE	1	SNV			1										1	.	TGT	.	.																					152763259
SCAF8	22828	.	GRCh37	6	155109182	155109182	+	Intron	SNP	T	T	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.321+26T>G			ENST00000367178		224	216	7	197	192	2	SCAF8,intron_variant,,ENST00000367178,NM_014892.3,NM_001286194.1;SCAF8,intron_variant,,ENST00000367186,NM_001286189.1;SCAF8,intron_variant,,ENST00000417268,NM_001286188.1,NM_001286199.1;SCAF8,intron_variant,,ENST00000461219,;SCAF8,intron_variant,,ENST00000464628,;	G	ENSG00000213079	ENST00000367178	Transcript	intron_variant							1		1	SCAF8	HGNC	20959	protein_coding	YES	CCDS5247.1	ENSP00000356146	Q9UPN6	Q9H8B2,Q8NDE9	UPI0000070A1C	NM_014892.3,NM_001286194.1				4/19																		MODIFIER	1	SNV														.	GTT	.	.																					155109182
FNDC1	84624	.	GRCh37	6	159653544	159653544	+	Missense_Mutation	SNP	G	G	A	rs139265083		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.2000G>A	p.Arg667Gln	p.R667Q	ENST00000297267	11/23	19	11	7	7			FNDC1,missense_variant,p.Arg667Gln,ENST00000297267,NM_032532.2;FNDC1,missense_variant,p.Arg604Gln,ENST00000340366,;FNDC1,missense_variant,p.Arg563Gln,ENST00000329629,;	A	ENSG00000164694	ENST00000297267	Transcript	missense_variant	2200/6552	2000/5685	667/1894	R/Q	cGg/cAg	rs139265083	1		1	FNDC1	HGNC	21184	protein_coding	YES	CCDS47512.1	ENSP00000297267	Q4ZHG4		UPI0000579B80	NM_032532.2	tolerated_low_confidence(0.2)	benign(0.009)	11/23		PANTHER:PTHR23197:SF8,PANTHER:PTHR23197	0.0134	0.0015	0.0317		0.001	0.0278	0.0143	0.007143	0.03748								MODERATE	1	SNV														.	CGG	.	.												0.02583	0.005546	0.01721	0.08306	0.0001126	0.01069	0.03629	0.03849	0.01242	159653544
MAD1L1	8379	.	GRCh37	7	1976432	1976432	+	Silent	SNP	C	C	T	rs1801550		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1698G>A	p.Ala566=	p.A566=	ENST00000406869	17/19	29	15	14	4			MAD1L1,synonymous_variant,p.Ala566=,ENST00000406869,;MAD1L1,synonymous_variant,p.Ala566=,ENST00000399654,NM_001013837.1,NM_003550.2,NM_001013836.1;MAD1L1,synonymous_variant,p.Ala566=,ENST00000265854,;MAD1L1,synonymous_variant,p.Ala474=,ENST00000402746,;MAD1L1,synonymous_variant,p.Ala22=,ENST00000437877,;MAD1L1,synonymous_variant,p.Ala117=,ENST00000450235,;	T	ENSG00000002822	ENST00000406869	Transcript	synonymous_variant	2256/2991	1698/2157	566/718	A	gcG/gcA	rs1801550	1		-1	MAD1L1	HGNC	6762	protein_coding	YES	CCDS43539.1	ENSP00000385334	Q9Y6D9	C9K086,C9JX80,C9JTA2,C9JKI7,C9JJ38,C9J9H5	UPI0000072C4D				17/19		Superfamily:0053432,Coiled-coils_(Ncoils):Coil,Pfam:PF05557,PANTHER:PTHR23168,PANTHER:PTHR23168:SF0	0.0379	0.0023	0.111		0.006	0.0308	0.0746	0.009403	0.03887								LOW	1	SNV														.	CCG	.	.												0.05402	0.007194	0.1634	0.0293	0.001668	0.02928	0.0354	0.05231	0.07064	1976432
TTYH3	80727	.	GRCh37	7	2691610	2691610	+	Intron	SNP	G	A	A	rs13225657		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.872-211G>A			ENST00000258796		4	0	4	3			TTYH3,intron_variant,,ENST00000258796,NM_025250.2;TTYH3,intron_variant,,ENST00000403167,;TTYH3,intron_variant,,ENST00000407643,;TTYH3,downstream_gene_variant,,ENST00000400376,;TTYH3,upstream_gene_variant,,ENST00000429448,;TTYH3,downstream_gene_variant,,ENST00000477439,;TTYH3,upstream_gene_variant,,ENST00000498454,;	A	ENSG00000136295	ENST00000258796	Transcript	intron_variant						rs13225657	1		1	TTYH3	HGNC	22222	protein_coding	YES	CCDS34588.1	ENSP00000258796	Q9C0H2		UPI000020E9F9	NM_025250.2				7/13		0.2266	0.3033	0.1873		0.1716	0.2316	0.2025										MODIFIER	1	SNV														.	CGT	.	.																					2691610
RAPGEF5	9771	.	GRCh37	7	22200248	22200248	+	Intron	SNP	C	C	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.970-15G>A			ENST00000344041		114	101	13	96	96	0	RAPGEF5,intron_variant,,ENST00000344041,NM_012294.3;RAPGEF5,intron_variant,,ENST00000401957,;RAPGEF5,intron_variant,,ENST00000458533,;RAPGEF5,intron_variant,,ENST00000451559,;	T	ENSG00000136237	ENST00000344041	Transcript	intron_variant							1		-1	RAPGEF5	HGNC	16862	protein_coding	YES	CCDS55093.1	ENSP00000343656		C9JBS6,A8MQ07	UPI0000EA87E4	NM_012294.3				13/25																		MODIFIER	1	SNV														.	ACA	.	.																					22200248
STK17A	9263	.	GRCh37	7	43622806	43622806	+	5'UTR	SNP	T	T	C	rs10251937		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.-37T>C			ENST00000319357	1/7	9	3	6	4			STK17A,5_prime_UTR_variant,,ENST00000319357,NM_004760.2;AC011738.1,downstream_gene_variant,,ENST00000516499,;STK17A,intron_variant,,ENST00000462448,;,regulatory_region_variant,,ENSR00000211699,;,TF_binding_site_variant,,ENSM00525188203,;,TF_binding_site_variant,,ENSM00523322797,;,TF_binding_site_variant,,ENSM00807623128,;	C	ENSG00000164543	ENST00000319357	Transcript	5_prime_UTR_variant	143/3368					rs10251937	1		1	STK17A	HGNC	11395	protein_coding	YES	CCDS5470.1	ENSP00000319192	Q9UEE5	Q86UI9,Q75MK4	UPI00001405A1	NM_004760.2			1/7			0.3698	0.4418	0.4827		0.2857	0.3787	0.2699	0.4549	0.37								MODIFIER	1	SNV														.	GTG	.	.												0.3795	0.4622	0.5169	0.3185	0.2822	0.3584	0.3756	0.3648	0.298	43622806
NPC1L1	29881	.	GRCh37	7	44580876	44580876	+	5'UTR	SNP	G	G	T	rs41279633		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.-18C>A			ENST00000289547	1/20	11	3	8	7			NPC1L1,5_prime_UTR_variant,,ENST00000289547,NM_013389.2;NPC1L1,5_prime_UTR_variant,,ENST00000381160,NM_001101648.1;NPC1L1,5_prime_UTR_variant,,ENST00000546276,;NPC1L1,5_prime_UTR_variant,,ENST00000423141,;	T	ENSG00000015520	ENST00000289547	Transcript	5_prime_UTR_variant	39/5048					rs41279633	1		-1	NPC1L1	HGNC	7898	protein_coding	YES	CCDS5491.1	ENSP00000289547	Q9UHC9		UPI000013DF88	NM_013389.2			1/20			0.0653	0.0068	0.0821		0.0337	0.1431	0.0849	0.02946	0.127			21862702,28577571,29764733,24648913,19747803					MODIFIER	1	SNV			1										1	.	GGT	.	.												0.1201	0.02765	0.05961	0.1573	0.02186	0.2193	0.158	0.1255	0.09816	44580876
ADCY1	107	.	GRCh37	7	45717850	45717850	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1886T>G	p.Leu629Arg	p.L629R	ENST00000297323	10/20	392	382	10	274	272	1	ADCY1,missense_variant,p.Leu629Arg,ENST00000297323,NM_021116.2;	G	ENSG00000164742	ENST00000297323	Transcript	missense_variant	1908/12503	1886/3360	629/1119	L/R	cTa/cGa		1		1	ADCY1	HGNC	232	protein_coding	YES	CCDS34631.1	ENSP00000297323	Q08828	Q8NFM5,D3DVL8	UPI0000199C4A	NM_021116.2	deleterious(0)	probably_damaging(0.971)	10/20		PANTHER:PTHR11920,PANTHER:PTHR11920:SF20,Transmembrane_helices:TMhelix																	MODERATE	1	SNV													1	.	CTA	.	.																					45717850
PKD1L1	168507	.	GRCh37	7	47894517	47894517	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.4822C>A	p.Pro1608Thr	p.P1608T	ENST00000289672	30/57	98	94	4	112	112	0	PKD1L1,missense_variant,p.Pro1608Thr,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,;	T	ENSG00000158683	ENST00000289672	Transcript	missense_variant	4873/9092	4822/8550	1608/2849	P/T	Cct/Act		1		-1	PKD1L1	HGNC	18053	protein_coding	YES	CCDS34633.1	ENSP00000289672	Q8TDX9		UPI0000130FA9	NM_138295.3	tolerated(0.19)	benign(0.195)	30/57		PANTHER:PTHR10877,PANTHER:PTHR10877:SF32																	MODERATE	1	SNV													1	.	GGT	.	.																					47894517
SHFM1	7979	.	GRCh37	7	96339155	96339155	+	5'UTR	SNP	C	C	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.-80G>T			ENST00000248566	1/3	65	49	16	44	43	0	SHFM1,5_prime_UTR_variant,,ENST00000248566,NM_006304.1;SHFM1,5_prime_UTR_variant,,ENST00000413065,;SHFM1,5_prime_UTR_variant,,ENST00000444799,;SHFM1,5_prime_UTR_variant,,ENST00000417009,;SHFM1,non_coding_transcript_exon_variant,,ENST00000488005,;SHFM1,non_coding_transcript_exon_variant,,ENST00000476463,;SHFM1,upstream_gene_variant,,ENST00000466986,;SHFM1,5_prime_UTR_variant,,ENST00000449279,;,regulatory_region_variant,,ENSR00000215458,;,TF_binding_site_variant,,ENSM00524523721,;,TF_binding_site_variant,,ENSM00523505996,;,TF_binding_site_variant,,ENSM00525166294,;,TF_binding_site_variant,,ENSM00525129860,;,TF_binding_site_variant,,ENSM00531705029,;,TF_binding_site_variant,,ENSM00532344145,;,TF_binding_site_variant,,ENSM00531930650,;,TF_binding_site_variant,,ENSM00523184903,;,TF_binding_site_variant,,ENSM00908234473,;,TF_binding_site_variant,,ENSM00525146268,;,TF_binding_site_variant,,ENSM00523947106,;	A	ENSG00000127922	ENST00000248566	Transcript	5_prime_UTR_variant	49/807						1		-1	SHFM1	HGNC	10845	protein_coding	YES	CCDS5646.1	ENSP00000248566	P60896	Q6IBB7	UPI000000162C	NM_006304.1			1/3																			MODIFIER	1	SNV													1	.	TCA	.	.																					96339155
CDHR3	222256	.	GRCh37	7	105636709	105636709	+	Missense_Mutation	SNP	G	G	A	rs200019471		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.622G>A	p.Val208Met	p.V208M	ENST00000317716	6/19	40	30	10	27	27	0	CDHR3,missense_variant,p.Val208Met,ENST00000542731,;CDHR3,missense_variant,p.Val208Met,ENST00000317716,NM_152750.4;CDHR3,missense_variant,p.Val120Met,ENST00000478080,;CDHR3,5_prime_UTR_variant,,ENST00000343407,;CDHR3,intron_variant,,ENST00000541203,;CDHR3,intron_variant,,ENST00000461766,;CDHR3,intron_variant,,ENST00000470188,;CDHR3,intron_variant,,ENST00000488386,;CDHR3,intron_variant,,ENST00000496633,;	A	ENSG00000128536	ENST00000317716	Transcript	missense_variant	702/3813	622/2658	208/885	V/M	Gtg/Atg	rs200019471	1		1	CDHR3	HGNC	26308	protein_coding	YES	CCDS47684.1	ENSP00000325954	Q6ZTQ4	E7EQG5	UPI00001C0C6E	NM_152750.4	tolerated(0.1)	probably_damaging(0.95)	6/19		Gene3D:2.60.40.60,Pfam:PF00028,PROSITE_profiles:PS50268,PANTHER:PTHR24027,PANTHER:PTHR24027:SF289,SMART:SM00112,Superfamily:SSF49313								0.0002548	0.0002414								MODERATE	1	SNV														.	CGT	.	.												0.0002156	0.0001322	0.000117	0.0001005		0.0009368	0.0002337			105636709
SLC13A1	6561	.	GRCh37	7	122769396	122769396	+	Intron	SNP	G	G	C	rs201876307		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.1031+41C>G			ENST00000194130		109	97	12	88	0	0	SLC13A1,intron_variant,,ENST00000194130,NM_022444.3;SLC13A1,intron_variant,,ENST00000539873,;SLC13A1,intron_variant,,ENST00000427975,;SLC13A1,intron_variant,,ENST00000439260,;	C	ENSG00000081800	ENST00000194130	Transcript	intron_variant						rs201876307,COSV52010231	1		-1	SLC13A1	HGNC	10916	protein_coding	YES	CCDS5786.1	ENSP00000194130	Q9BZW2	Q75MH3,Q75LT0,A4D0X1	UPI0000049F9D	NM_022444.3				9/14												0,1						MODIFIER	1	SNV			0,1											.	TGT	.	.												0.2094	0.03984	0.1858	0.1829	0.2843	0.2473	0.228	0.2109	0.1928	122769396
ATP6V0A4	50617	.	GRCh37	7	138391207	138391207	+	3'UTR	SNP	G	G	A	rs55832008		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.*162C>T			ENST00000310018	22/22	7	1	6	4			ATP6V0A4,3_prime_UTR_variant,,ENST00000310018,NM_020632.2,NM_130840.2;ATP6V0A4,3_prime_UTR_variant,,ENST00000393054,NM_130841.2;ATP6V0A4,downstream_gene_variant,,ENST00000353492,;UQCRFS1P2,downstream_gene_variant,,ENST00000426701,;,regulatory_region_variant,,ENSR00001733747,;	A	ENSG00000105929	ENST00000310018	Transcript	3_prime_UTR_variant	2968/3135					rs55832008	1		-1	ATP6V0A4	HGNC	866	protein_coding	YES	CCDS5849.1	ENSP00000308122	Q9HBG4		UPI000013CDFD	NM_020632.2,NM_130840.2			22/22			0.0513	0.0061	0.1052		0.001	0.1372	0.0378			likely_benign							MODIFIER	1	SNV			1										1	.	CGT	.	.																					138391207
ABCF2	10061	.	GRCh37	7	150915788	150915788	+	Intron	SNP	A	A	C	rs200403284		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1137+52T>G			ENST00000222388		228	198	29	152	151	1	ABCF2,intron_variant,,ENST00000222388,NM_005692.4;ABCF2,intron_variant,,ENST00000287844,NM_007189.2;ABCF2,downstream_gene_variant,,ENST00000441774,;ABCF2,downstream_gene_variant,,ENST00000468073,;ABCF2,intron_variant,,ENST00000473874,;	C	ENSG00000033050	ENST00000222388	Transcript	intron_variant						rs200403284	1		-1	ABCF2	HGNC	71	protein_coding	YES	CCDS5922.1	ENSP00000222388		Q75MJ1,C9JZV3,C9JHK9	UPI000004C4C9	NM_005692.4				9/15		0.0072	0.0083	0.0101		0.006	0.0089	0.0031										MODIFIER	1	SNV														.	CAC	.	.												0.0002571	0.002131	2.912e-05				0.0002224	0.0006564		150915788
TNFRSF10C	8794	.	GRCh37	8	22974325	22974325	+	Silent	SNP	G	A	A	rs11780493		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.561G>A	p.Pro187=	p.P187=	ENST00000356864	5/5	165	36	129	90			TNFRSF10C,synonymous_variant,p.Pro187=,ENST00000356864,NM_003841.3;TNFRSF10C,synonymous_variant,p.Pro85=,ENST00000540813,;TNFRSF10C,downstream_gene_variant,,ENST00000520607,;TNFRSF10C,3_prime_UTR_variant,,ENST00000517558,;TNFRSF10C,downstream_gene_variant,,ENST00000518135,;	A	ENSG00000173535	ENST00000356864	Transcript	synonymous_variant	1093/1718	561/780	187/259	P	ccG/ccA	rs11780493	1		1	TNFRSF10C	HGNC	11906	protein_coding	YES	CCDS6037.1	ENSP00000349324	O14798	F5H6H7	UPI00001AF00A	NM_003841.3			5/5		Low_complexity_(Seg):seg,PANTHER:PTHR23097,PANTHER:PTHR23097:SF96																	LOW	1	SNV														.	CGG	.	.												0.4882	0.1788	0.5137	0.2202	0.5479	0.6146	0.5293	0.4495	0.3484	22974325
TEX15	56154	.	GRCh37	8	30705004	30705004	+	Silent	SNP	G	G	A	rs574770017		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.1530C>T	p.Asn510=	p.N510=	ENST00000256246	1/4	283	276	7	232	232	0	TEX15,synonymous_variant,p.Asn510=,ENST00000256246,NM_031271.3;TEX15,downstream_gene_variant,,ENST00000523186,;	A	ENSG00000133863	ENST00000256246	Transcript	synonymous_variant	1605/10187	1530/8370	510/2789	N	aaC/aaT	rs574770017	1		-1	TEX15	HGNC	11738	protein_coding	YES	CCDS6080.1	ENSP00000256246	Q9BXT5	D3DSV6	UPI000013CEF9	NM_031271.3			1/4		PANTHER:PTHR22380,PANTHER:PTHR22380:SF1	0.0008				0.004												LOW	1	SNV													1	.	CGT	.	.												6.425e-05				0.0006537		8.916e-06		9.897e-05	30705004
SGK3	23678	.	GRCh37	8	67753176	67753176	+	Intron	SNP	C	C	A	rs994230761		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.892-83C>A			ENST00000396596		70	.	.	56	.	.	SGK3,intron_variant,,ENST00000345714,;SGK3,intron_variant,,ENST00000396596,NM_013257.4;C8orf44-SGK3,intron_variant,,ENST00000519289,NM_001204173.1;SGK3,intron_variant,,ENST00000520976,NM_170709.2;SGK3,intron_variant,,ENST00000521198,NM_001033578.2;SGK3,intron_variant,,ENST00000522398,;SGK3,downstream_gene_variant,,ENST00000519396,;SGK3,downstream_gene_variant,,ENST00000521152,;SGK3,non_coding_transcript_exon_variant,,ENST00000523260,;SGK3,intron_variant,,ENST00000521435,;	A	ENSG00000104205	ENST00000396596	Transcript	intron_variant						rs994230761	2		1	SGK3	HGNC	10812	protein_coding	YES	CCDS6195.1	ENSP00000379842	Q96BR1	Q6FHV7,E5RK28,E5RJV7,E5RHR8	UPI000013591F	NM_013257.4				12/16																		MODIFIER	1	SNV														.	TCA	.	.																					67753176
COL14A1	7373	.	GRCh37	8	121344960	121344960	+	Missense_Mutation	SNP	G	G	A	rs370064596		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.4771G>A	p.Ala1591Thr	p.A1591T	ENST00000297848	42/48	280	170	110	183	182	0	COL14A1,missense_variant,p.Ala1591Thr,ENST00000297848,NM_021110.2;COL14A1,missense_variant,p.Ala1496Thr,ENST00000247781,;COL14A1,missense_variant,p.Ala1591Thr,ENST00000309791,;	A	ENSG00000187955	ENST00000297848	Transcript	missense_variant	5041/6466	4771/5391	1591/1796	A/T	Gcc/Acc	rs370064596	1		1	COL14A1	HGNC	2191	protein_coding	YES	CCDS34938.1	ENSP00000297848	Q05707		UPI000046D377	NM_021110.2	tolerated(0.05)	benign(0.009)	42/48		Pfam:PF01391,PANTHER:PTHR22992,PANTHER:PTHR22992:SF89								0.000227									MODERATE	1	SNV													1	.	CGC	.	.												1.202e-05		2.907e-05			4.672e-05			3.282e-05	121344960
TSNARE1	203062	.	GRCh37	8	143400081	143400081	+	Intron	SNP	C	C	T	rs572954039		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.894-86G>A			ENST00000307180		49	38	11	11	11	0	TSNARE1,intron_variant,,ENST00000307180,NM_145003.3;TSNARE1,intron_variant,,ENST00000519651,;TSNARE1,intron_variant,,ENST00000520166,;TSNARE1,intron_variant,,ENST00000524325,;TSNARE1,intron_variant,,ENST00000518928,;	T	ENSG00000171045	ENST00000307180	Transcript	intron_variant						rs572954039	1		-1	TSNARE1	HGNC	26437	protein_coding	YES	CCDS6384.1	ENSP00000303437	Q96NA8	E5RHW3,A0AVG3	UPI00001AEE5E	NM_145003.3				6/13																		MODIFIER	1	SNV														.	ACG	.	.																					143400081
MROH6	642475	.	GRCh37	8	144649690	144649690	+	Intron	SNP	C	T	T	rs13254590		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1934-55G>A			ENST00000398882		9	1	8	4			MROH6,intron_variant,,ENST00000398882,NM_001100878.1;MROH6,intron_variant,,ENST00000524906,;MROH6,intron_variant,,ENST00000532862,;MROH6,intron_variant,,ENST00000533679,;MROH6,intron_variant,,ENST00000534459,;GSDMD,downstream_gene_variant,,ENST00000262580,NM_024736.6;GSDMD,downstream_gene_variant,,ENST00000525208,;GSDMD,downstream_gene_variant,,ENST00000526406,NM_001166237.1;MROH6,downstream_gene_variant,,ENST00000529971,;GSDMD,downstream_gene_variant,,ENST00000533063,;MROH6,intron_variant,,ENST00000532704,;MROH6,downstream_gene_variant,,ENST00000533582,;MROH6,intron_variant,,ENST00000533083,;MROH6,intron_variant,,ENST00000533210,;GSDMD,downstream_gene_variant,,ENST00000524846,;GSDMD,downstream_gene_variant,,ENST00000526469,;GSDMD,downstream_gene_variant,,ENST00000528475,;GSDMD,downstream_gene_variant,,ENST00000531173,;GSDMD,downstream_gene_variant,,ENST00000531184,;MROH6,upstream_gene_variant,,ENST00000533120,;,regulatory_region_variant,,ENSR00000417890,;	T	ENSG00000204839	ENST00000398882	Transcript	intron_variant						rs13254590,COSV52796344	1		-1	MROH6	HGNC	27814	protein_coding	YES	CCDS47928.1	ENSP00000381857	A6NGR9	E9PJR4	UPI0000DD7EFB	NM_001100878.1				13/13		0.7893	0.6044	0.8487		0.9643	0.7724	0.8344				0,1						MODIFIER	1	SNV			0,1											.	GCC	.	.																					144649690
KCNV2	169522	.	GRCh37	9	2718534	2718534	+	Silent	SNP	C	G	G	rs12237048		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.795C>G	p.Ala265=	p.A265=	ENST00000382082	1/2	6	0	6	4	4	0	KCNV2,synonymous_variant,p.Ala265=,ENST00000382082,NM_133497.3;KIAA0020,downstream_gene_variant,,ENST00000490444,;	G	ENSG00000168263	ENST00000382082	Transcript	synonymous_variant	1033/2186	795/1638	265/545	A	gcC/gcG	rs12237048	1		1	KCNV2	HGNC	19698	protein_coding	YES	CCDS6447.1	ENSP00000371514	Q8TDN2		UPI0000048D8E	NM_133497.3			1/2		Gene3D:1.20.120.350,Prints:PR00169,PANTHER:PTHR11537,PANTHER:PTHR11537:SF40,Superfamily:SSF81324,Transmembrane_helices:TMhelix	0.4800	0.3502	0.549		0.7173	0.4742	0.3681	0.3797	0.4642	benign		25741868,23757202					LOW	1	SNV			1										1	.	CCT	.	.												0.4839	0.3743	0.5651	0.4583	0.7171	0.521	0.4634	0.4738	0.3661	2718534
FREM1	158326	.	GRCh37	9	14737583	14737583	+	Silent	SNP	G	G	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.6351C>T	p.Asp2117=	p.D2117=	ENST00000422223	38/38	76	52	24	87	87	0	FREM1,synonymous_variant,p.Asp2118=,ENST00000380881,;FREM1,synonymous_variant,p.Asp2117=,ENST00000422223,NM_144966.5;FREM1,synonymous_variant,p.Asp2117=,ENST00000380880,;FREM1,synonymous_variant,p.Asp653=,ENST00000380894,NM_001177704.1;FREM1,3_prime_UTR_variant,,ENST00000380875,;FREM1,3_prime_UTR_variant,,ENST00000427623,;	A	ENSG00000164946	ENST00000422223	Transcript	synonymous_variant	7167/10086	6351/6540	2117/2179	D	gaC/gaT		1		-1	FREM1	HGNC	23399	protein_coding	YES	CCDS47952.1	ENSP00000412940	Q5H8C1		UPI000057A218	NM_144966.5			38/38		Superfamily:SSF56436,SMART:SM00034,Pfam:PF00059,Gene3D:3.10.100.10,PANTHER:PTHR11878,PANTHER:PTHR11878:SF24,PROSITE_profiles:PS50041																	LOW	1	SNV													1	.	GGT	.	.																					14737583
ADAMTSL1	92949	.	GRCh37	9	18889789	18889789	+	Intron	SNP	G	G	A	rs34099646		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.4643+43G>A			ENST00000380548		19	6	13	8			ADAMTSL1,intron_variant,,ENST00000380538,;ADAMTSL1,intron_variant,,ENST00000380545,;ADAMTSL1,intron_variant,,ENST00000380548,NM_001040272.5;ADAMTSL1,intron_variant,,ENST00000380559,;ADAMTSL1,intron_variant,,ENST00000388710,;ADAMTSL1,intron_variant,,ENST00000542621,;	A	ENSG00000178031	ENST00000380548	Transcript	intron_variant						rs34099646	1		1	ADAMTSL1	HGNC	14632	protein_coding	YES	CCDS47954.1	ENSP00000369921	Q8N6G6	H7BYE3	UPI000004FD83	NM_001040272.5				25/28		0.4750	0.5227	0.4539		0.5169	0.4751	0.3824	0.4761	0.4373								MODIFIER	1	SNV													1	.	AGG	.	.												0.4473	0.4979	0.3868	0.3548	0.5226	0.5433	0.4434	0.4183	0.369	18889789
CNTFR	1271	.	GRCh37	9	34564705	34564705	+	Missense_Mutation	SNP	C	C	T	rs753060196		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.211G>A	p.Gly71Ser	p.G71S	ENST00000378980	4/10	143	121	21	55	54	0	CNTFR,missense_variant,p.Gly71Ser,ENST00000378980,NM_147164.2,NM_001207011.1;CNTFR,missense_variant,p.Gly71Ser,ENST00000351266,NM_001842.4;CNTFR,missense_variant,p.Gly71Ser,ENST00000417345,;CNTFR-AS1,upstream_gene_variant,,ENST00000436360,;CNTFR-AS1,upstream_gene_variant,,ENST00000438244,;CNTFR-AS1,upstream_gene_variant,,ENST00000453642,;CNTFR-AS1,upstream_gene_variant,,ENST00000454187,;	T	ENSG00000122756	ENST00000378980	Transcript	missense_variant	505/2052	211/1119	71/372	G/S	Ggc/Agc	rs753060196,COSV63634912	1		-1	CNTFR	HGNC	2170	protein_coding	YES	CCDS6558.1	ENSP00000368265	P26992	Q5T8H6,B3KXJ2	UPI0000000DBD	NM_147164.2,NM_001207011.1	deleterious(0.02)	probably_damaging(0.997)	4/10		Superfamily:SSF48726,SMART:SM00409,SMART:SM00408,Gene3D:2.60.40.10,PANTHER:PTHR23036,PANTHER:PTHR23036:SF93,PROSITE_profiles:PS50835											0,1						MODERATE	1	SNV			0,1											.	CCG	.	.												1.993e-05					4.628e-05	3.531e-05			34564705
RP11-764K9.4	0	.	GRCh37	9	68427793	68427793	+	3'Flank	SNP	G	G	T	rs1163742084		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																			ENST00000376334		392	379	13	287	283	1	RP11-764K9.4,downstream_gene_variant,,ENST00000376334,;	T	ENSG00000215548	ENST00000376334	Transcript	downstream_gene_variant						rs1163742084	1	68	-1	RP11-764K9.4	Clone_based_vega_gene		unprocessed_pseudogene	YES																												MODIFIER	1	SNV														.	AGC	.	.																					68427793
FKBP15	23307	.	GRCh37	9	115934061	115934061	+	Intron	SNP	A	A	C	rs1176070245		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.2533-75T>G			ENST00000238256		57			59			FKBP15,intron_variant,,ENST00000238256,NM_015258.1;FKBP15,intron_variant,,ENST00000446284,;	C	ENSG00000119321	ENST00000238256	Transcript	intron_variant						rs1176070245	2		-1	FKBP15	HGNC	23397	protein_coding	YES	CCDS48007.1	ENSP00000238256	Q5T1M5	B4DZS8	UPI000022D996	NM_015258.1				23/27																		MODIFIER	1	SNV														.	CAC	.	.																					115934061
KIAA1217	56243	.	GRCh37	10	24498096	24498096	+	5'UTR	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.-27G>T			ENST00000376454	1/21	87	83	4	93	93	0	KIAA1217,5_prime_UTR_variant,,ENST00000376454,NM_019590.3;KIAA1217,5_prime_UTR_variant,,ENST00000458595,NM_001098501.1,NM_001282768.1;KIAA1217,5_prime_UTR_variant,,ENST00000376456,;KIAA1217,intron_variant,,ENST00000376462,NM_001098500.1;KIAA1217,upstream_gene_variant,,ENST00000376452,NM_001282767.1;,regulatory_region_variant,,ENSR00000025610,;	T	ENSG00000120549	ENST00000376454	Transcript	5_prime_UTR_variant	4/7381						1		1	KIAA1217	HGNC	25428	protein_coding	YES	CCDS31165.1	ENSP00000365637	Q5T5P2		UPI000013EC2A	NM_019590.3			1/21																			MODIFIER	1	SNV														.	CGA	.	.																					24498096
SYT15	83849	.	GRCh37	10	46961964	46961964	+	3'UTR	SNP	G	G	A	rs9422211		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.*6C>T			ENST00000374321	8/8	67	19	10	20	9	0	SYT15,3_prime_UTR_variant,,ENST00000374323,;SYT15,3_prime_UTR_variant,,ENST00000374321,NM_031912.4;SYT15,intron_variant,,ENST00000374325,NM_181519.2;SYT15,intron_variant,,ENST00000374328,;SYT15,intron_variant,,ENST00000503753,;SYT15,downstream_gene_variant,,ENST00000512997,;RP11-38L15.3,intron_variant,,ENST00000506914,;SYT15,upstream_gene_variant,,ENST00000449358,;,regulatory_region_variant,,ENSR00001521007,;	A	ENSG00000204176	ENST00000374321	Transcript	3_prime_UTR_variant	1339/1369					rs9422211	1		-1	SYT15	HGNC	17167	protein_coding	YES	CCDS44376.1	ENSP00000363441	Q9BQS2		UPI00001AA161	NM_031912.4			8/8										0.0252	0.1252								MODIFIER	1	SNV														.	CGA	.	.												0.1188	0.02564	0.07773	0.0664	0.05623	0.1406	0.1414	0.118	0.1777	46961964
ANK3	288	.	GRCh37	10	61834851	61834851	+	Missense_Mutation	SNP	G	G	C	rs777939067		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.5788C>G	p.Gln1930Glu	p.Q1930E	ENST00000280772	37/44	378	207	170	217	217	0	ANK3,missense_variant,p.Gln1930Glu,ENST00000280772,NM_020987.3;ANK3,intron_variant,,ENST00000355288,NM_001149.3;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000373827,NM_001204403.1;ANK3,intron_variant,,ENST00000503366,NM_001204404.1;ANK3,intron_variant,,ENST00000511043,;	C	ENSG00000151150	ENST00000280772	Transcript	missense_variant	5980/16874	5788/13134	1930/4377	Q/E	Caa/Gaa	rs777939067,COSV55079809	1		-1	ANK3	HGNC	494	protein_coding	YES	CCDS7258.1	ENSP00000280772	Q12955	D6RFK6,D6RBY7,B1AQT1	UPI0000141BA9	NM_020987.3	tolerated_low_confidence(0.1)	benign(0.015)	37/44		PANTHER:PTHR24123,PANTHER:PTHR24123:SF15											0,1						MODERATE	1	SNV			0,1										1	.	TGG	.	.												3.993e-06								3.268e-05	61834851
PTEN	5728	.	GRCh37	10	89692904	89692904	+	Nonsense_Mutation	SNP	C	C	T	rs121909224		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	5/9	249	233	16	195	193	0	PTEN,stop_gained,p.Arg130Ter,ENST00000371953,NM_000314.4;PTEN,non_coding_transcript_exon_variant,,ENST00000498703,;	T	ENSG00000171862	ENST00000371953	Transcript	stop_gained	1745/9027	388/1212	130/403	R/*	Cga/Tga	rs121909224,CM094223,CM971273,COSV64288384,COSV64288463,COSV64297940,COSV64311187	1		1	PTEN	HGNC	9588	protein_coding	YES	CCDS31238.1	ENSP00000361021	P60484	F6KD01,H6WA51,H6WA46	UPI00001328C5	NM_000314.4			5/9		Gene3D:3.90.190.10,Pfam:PF00782,PIRSF:PIRSF038025,PROSITE_patterns:PS00383,PROSITE_profiles:PS51181,PANTHER:PTHR12305,SMART:SM00404,Superfamily:SSF52799										likely_pathogenic,pathogenic	0,0,0,1,1,1,1	23757202,26619011,25157968,28526761,9259288,10923032,11504908,20085938,21194675,23335809,9856571,11274365,17286265,18767981,21824802,21956414,22266152,23470840,29784605					HIGH	1	SNV			1,1,1,1,1,1,1										1	.	ACG	.	.												1.193e-05		2.891e-05				8.797e-06		3.266e-05	89692904
CYP2C18	1562	.	GRCh37	10	96448129	96448129	+	Intron	SNP	A	G	G	rs1926706		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	G																c.481+98A>G			ENST00000285979		16	0	16	4			CYP2C18,intron_variant,,ENST00000285979,NM_000772.2;CYP2C18,intron_variant,,ENST00000339022,NM_001128925.1;CYP2C19,intron_variant,,ENST00000464755,;	G	ENSG00000108242	ENST00000285979	Transcript	intron_variant						rs1926706	1		1	CYP2C18	HGNC	2620	protein_coding	YES	CCDS7435.1	ENSP00000285979	P33260	Q16750	UPI000013DE1D	NM_000772.2				3/8		0.5086	0.6604	0.2767		0.4246	0.4433	0.6217					17048007					MODIFIER	1	SNV														.	CAT	.	.																					96448129
PNLIPRP2	5408	.	GRCh37	10	118387282	118387282	+	Silent	SNP	A	G	G	rs11544712		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.474A>G	p.Leu158=	p.L158=	ENST00000537242	7/14	19	2	17	5	5	0	PNLIPRP2,synonymous_variant,p.Leu158=,ENST00000537242,NM_005396.4;PNLIPRP2,non_coding_transcript_exon_variant,,ENST00000298771,;PNLIPRP2,non_coding_transcript_exon_variant,,ENST00000429325,;PNLIPRP2,downstream_gene_variant,,ENST00000444825,;PNLIPRP2,stop_lost,p.Ter158TrpextTer?,ENST00000433618,;	G	ENSG00000165862	ENST00000537242	Transcript	synonymous_variant	500/1479	474/1407	158/468	L	ctA/ctG	rs11544712	1		1	PNLIPRP2	HGNC	9157	protein_coding	YES		ENSP00000446346		F5H1V6	UPI0000D60FDD	NM_005396.4			7/14		Gene3D:3.40.50.1820,Pfam:PF00151,PIRSF:PIRSF000865,Prints:PR00821,PANTHER:PTHR11610,PANTHER:PTHR11610:SF85,Superfamily:SSF53474	0.3622	0.2375	0.4193		0.5784	0.338	0.2924	0.2387	0.3014								LOW	1	SNV														.	TAG	.	.												0.3006	0.2366	0.4472	0.4317	0.4881	0.2717	0.2923	0.3138	0.2044	118387282
FGFR2	2263	.	GRCh37	10	123310734	123310734	+	Intron	SNP	A	A	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.624+70T>G			ENST00000457416		54	32	21	41	40	0	FGFR2,intron_variant,,ENST00000336553,;FGFR2,intron_variant,,ENST00000346997,;FGFR2,intron_variant,,ENST00000351936,;FGFR2,intron_variant,,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,intron_variant,,ENST00000357555,NM_023029.2,NM_001144915.1;FGFR2,intron_variant,,ENST00000358487,NM_000141.4;FGFR2,intron_variant,,ENST00000359354,;FGFR2,intron_variant,,ENST00000360144,NM_001144919.1;FGFR2,intron_variant,,ENST00000369056,NM_001144913.1;FGFR2,intron_variant,,ENST00000369058,;FGFR2,intron_variant,,ENST00000369059,;FGFR2,intron_variant,,ENST00000369060,NM_001144917.1;FGFR2,intron_variant,,ENST00000369061,NM_001144914.1;FGFR2,intron_variant,,ENST00000457416,NM_022970.3;FGFR2,intron_variant,,ENST00000490349,;FGFR2,intron_variant,,ENST00000604236,;	C	ENSG00000066468	ENST00000457416	Transcript	intron_variant							1		-1	FGFR2	HGNC	3689	protein_coding	YES	CCDS7620.2	ENSP00000410294	P21802	Q9UMB0,Q9UEH2,D3DRD6	UPI000002A99A	NM_022970.3				5/17																		MODIFIER	1	SNV													1	.	CAA	.	.																					123310734
TNNT3	7140	.	GRCh37	11	1958016	1958016	+	Intron	SNP	C	C	T	rs72846743		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.682-177C>T			ENST00000278317		10	3	7	3			TNNT3,intron_variant,,ENST00000278317,NM_006757.3;TNNT3,intron_variant,,ENST00000344578,;TNNT3,intron_variant,,ENST00000360603,;TNNT3,intron_variant,,ENST00000381548,;TNNT3,intron_variant,,ENST00000381549,NM_001042782.2;TNNT3,intron_variant,,ENST00000381557,;TNNT3,intron_variant,,ENST00000381558,;TNNT3,intron_variant,,ENST00000381561,;TNNT3,intron_variant,,ENST00000381563,;TNNT3,intron_variant,,ENST00000381579,NM_001042780.2;TNNT3,intron_variant,,ENST00000381589,NM_001042781.2;TNNT3,intron_variant,,ENST00000397301,;TNNT3,intron_variant,,ENST00000397304,;TNNT3,intron_variant,,ENST00000446240,;TNNT3,downstream_gene_variant,,ENST00000453458,;TNNT3,upstream_gene_variant,,ENST00000473100,;TNNT3,downstream_gene_variant,,ENST00000492075,;TNNT3,downstream_gene_variant,,ENST00000493234,;	T	ENSG00000130595	ENST00000278317	Transcript	intron_variant						rs72846743	1		1	TNNT3	HGNC	11950	protein_coding	YES	CCDS7727.1	ENSP00000278317	P45378		UPI000013DB6C	NM_006757.3				14/15		0.0649	0.0204	0.0692		0.1032	0.0378	0.1104										MODIFIER	1	SNV													1	.	ACG	.	.																					1958016
OR51G1	79324	.	GRCh37	11	4945468	4945468	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.102C>A	p.Cys34Ter	p.C34*	ENST00000321961	1/1	78	74	4	99	98	0	OR51G1,stop_gained,p.Cys34Ter,ENST00000321961,NM_001005237.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,;	T	ENSG00000176879	ENST00000321961	Transcript	stop_gained	170/1107	102/966	34/321	C/*	tgC/tgA		1		-1	OR51G1	HGNC	14738	protein_coding	YES	CCDS31366.1	ENSP00000322546	Q8NGK1		UPI0000041B56	NM_001005237.1			1/1		Transmembrane_helices:TMhelix,PANTHER:PTHR26450,PANTHER:PTHR26450:SF140,Gene3D:1.20.1070.10,Superfamily:SSF81321,Prints:PR00237																	HIGH	1	SNV														.	AGC	.	.																					4945468
OR4C10P	0	.	GRCh37	11	48453787	48453787	+	RNA	SNP	G	A	A	rs4882063		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																n.913C>T			ENST00000434991	1/1	130	38	92	121			OR4C10P,non_coding_transcript_exon_variant,,ENST00000434991,;	A	ENSG00000184789	ENST00000434991	Transcript	non_coding_transcript_exon_variant	913/931					rs4882063	1		-1	OR4C10P	HGNC	14800	unprocessed_pseudogene	YES									1/1			0.4431	0.3306	0.5346		0.4256	0.6143	0.3722										MODIFIER	1	SNV														.	TGT	.	.																					48453787
ZFP91	80829	.	GRCh37	11	58381738	58381738	+	Missense_Mutation	SNP	T	T	A			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1024T>A	p.Tyr342Asn	p.Y342N	ENST00000316059	9/11	127	82	45	146	145	0	ZFP91,missense_variant,p.Tyr342Asn,ENST00000316059,NM_001197051.1,NM_053023.4;AP001350.1,upstream_gene_variant,,ENST00000601906,;ZFP91-CNTF,missense_variant,p.Tyr342Asn,ENST00000389919,;ZFP91-CNTF,missense_variant,p.Tyr169Asn,ENST00000422974,;	A	ENSG00000186660	ENST00000316059	Transcript	missense_variant	1195/5220	1024/1713	342/570	Y/N	Tat/Aat	COSV60161773	1		1	ZFP91	HGNC	14983	protein_coding	YES	CCDS31553.1	ENSP00000339030	Q96JP5	B4DIN6	UPI0000070D45	NM_001197051.1,NM_053023.4	deleterious(0)	possibly_damaging(0.829)	9/11		SMART:SM00355,Gene3D:3.30.160.60,PANTHER:PTHR11389:SF437,PANTHER:PTHR11389,PROSITE_profiles:PS50157											1						MODERATE	1	SNV			1											.	ATA	.	.																					58381738
RTN3	10313	.	GRCh37	11	63523458	63523458	+	Intron	SNP	T	T	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.2995-126T>G			ENST00000377819		36	32	4	80	0	0	RTN3,intron_variant,,ENST00000339997,NM_201428.2,NM_001265590.1;RTN3,intron_variant,,ENST00000341307,NM_201430.2;RTN3,intron_variant,,ENST00000354497,NM_001265591.1;RTN3,intron_variant,,ENST00000356000,NM_201429.2;RTN3,intron_variant,,ENST00000377819,NM_001265589.1;RTN3,intron_variant,,ENST00000537981,NM_006054.3;RTN3,intron_variant,,ENST00000540798,;RTN3,downstream_gene_variant,,ENST00000542238,;C11orf95,downstream_gene_variant,,ENST00000433688,;RTN3,intron_variant,,ENST00000536011,;	G	ENSG00000133318	ENST00000377819	Transcript	intron_variant							1		1	RTN3	HGNC	10469	protein_coding	YES	CCDS58141.1	ENSP00000367050	O95197		UPI00004546A2	NM_001265589.1				7/8																		MODIFIER	1	SNV														.	GTG	.	.																					63523458
FIBP	9158	.	GRCh37	11	65655337	65655337	+	Intron	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.284+68C>A			ENST00000338369		46	42	4	47	47	0	FIBP,intron_variant,,ENST00000338369,NM_198897.1;FIBP,intron_variant,,ENST00000357519,NM_004214.4;FIBP,intron_variant,,ENST00000533045,;CTSW,downstream_gene_variant,,ENST00000307886,NM_001335.3;FOSL1,downstream_gene_variant,,ENST00000312562,NM_005438.3;CCDC85B,upstream_gene_variant,,ENST00000312579,NM_006848.2;FOSL1,downstream_gene_variant,,ENST00000448083,;CTSW,downstream_gene_variant,,ENST00000526034,;CTSW,downstream_gene_variant,,ENST00000528419,;FOSL1,downstream_gene_variant,,ENST00000531493,;FOSL1,downstream_gene_variant,,ENST00000532401,;FIBP,intron_variant,,ENST00000426652,;FIBP,non_coding_transcript_exon_variant,,ENST00000442885,;FIBP,intron_variant,,ENST00000528937,;FIBP,intron_variant,,ENST00000532229,;FIBP,intron_variant,,ENST00000532679,;FIBP,intron_variant,,ENST00000533037,;FIBP,upstream_gene_variant,,ENST00000525765,;FIBP,upstream_gene_variant,,ENST00000531115,;FIBP,upstream_gene_variant,,ENST00000532934,;FIBP,upstream_gene_variant,,ENST00000534032,;,regulatory_region_variant,,ENSR00000040904,;	T	ENSG00000172500	ENST00000338369	Transcript	intron_variant							1		-1	FIBP	HGNC	3705	protein_coding	YES	CCDS8119.1	ENSP00000344572	O43427	B4DKH9	UPI000012A79E	NM_198897.1				2/9																		MODIFIER	1	SNV													1	.	TGT	.	.																					65655337
PPP6R3	55291	.	GRCh37	11	68331663	68331663	+	Intron	SNP	G	G	A	rs12804775		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.846-108G>A			ENST00000393801		10	5	5	6			PPP6R3,intron_variant,,ENST00000265636,NM_018312.4;PPP6R3,intron_variant,,ENST00000265637,;PPP6R3,intron_variant,,ENST00000393799,;PPP6R3,intron_variant,,ENST00000393800,NM_001164161.1,NM_001164163.1,NM_001164162.1;PPP6R3,intron_variant,,ENST00000393801,NM_001164160.1;PPP6R3,intron_variant,,ENST00000524845,;PPP6R3,intron_variant,,ENST00000524904,;PPP6R3,intron_variant,,ENST00000527403,;PPP6R3,intron_variant,,ENST00000529710,NM_001164164.1;PPP6R3,intron_variant,,ENST00000534190,;PPP6R3,intron_variant,,ENST00000534534,;PPP6R3,intron_variant,,ENST00000531432,;PPP6R3,upstream_gene_variant,,ENST00000526574,;	A	ENSG00000110075	ENST00000393801	Transcript	intron_variant						rs12804775	1		1	PPP6R3	HGNC	1173	protein_coding	YES	CCDS53671.1	ENSP00000377390	Q5H9R7	E9PNN8,E9PKG4,E9PK08,E9PJD8	UPI0000688150	NM_001164160.1				8/24		0.0459	0.0023	0.049		0.001	0.1083	0.0849										MODIFIER	1	SNV														.	CGC	.	.																					68331663
CCND1	595	.	GRCh37	11	69466115	69466115	+	3'UTR	SNP	C	A	A	rs7177		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.*65C>A			ENST00000227507	5/5	6	1	5	3			CCND1,3_prime_UTR_variant,,ENST00000227507,NM_053056.2;CCND1,downstream_gene_variant,,ENST00000536559,;ORAOV1,downstream_gene_variant,,ENST00000538554,;ORAOV1,downstream_gene_variant,,ENST00000542515,;ORAOV1,downstream_gene_variant,,ENST00000569105,;CCND1,non_coding_transcript_exon_variant,,ENST00000542367,;CCND1,downstream_gene_variant,,ENST00000545484,;	A	ENSG00000110092	ENST00000227507	Transcript	3_prime_UTR_variant	1180/4307					rs7177	1		1	CCND1	HGNC	1582	protein_coding	YES	CCDS8191.1	ENSP00000227507	P24385	Q9H014,Q6FI00,Q5MGB2	UPI0000001285	NM_053056.2			5/5			0.4910	0.1566	0.4179		0.8591	0.5626	0.5419					26959740,19372140,29963112,23125009,26621531,28596683,29113352,29599703,22406644,21107342					MODIFIER	1	SNV													1	.	CCC	.	.																					69466115
ATM	472	.	GRCh37	11	108119638	108119638	+	Intron	SNP	T	T	G	rs778167931		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1066-22T>G			ENST00000278616		21	17	4	37	0	0	ATM,intron_variant,,ENST00000278616,NM_000051.3;ATM,intron_variant,,ENST00000452508,;ATM,intron_variant,,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000527891,;ATM,upstream_gene_variant,,ENST00000525012,;ATM,upstream_gene_variant,,ENST00000533526,;	G	ENSG00000149311	ENST00000278616	Transcript	intron_variant						rs778167931	1		1	ATM	HGNC	795	protein_coding	YES	CCDS31669.1	ENSP00000278616	Q13315	M0QXY8,E9PRG7,E9PIN0	UPI0000DBEF44	NM_000051.3				8/62																		MODIFIER	1	SNV													1	.	GTG	.	.												0.02391	0.02367	0.009541	0.01404	0.01324	0.05466	0.02753	0.01436	0.0284	108119638
SIDT2	51092	.	GRCh37	11	117063930	117063930	+	Missense_Mutation	SNP	A	A	G			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.2167A>G	p.Ile723Val	p.I723V	ENST00000324225	23/26	179	124	55	131	129	0	SIDT2,missense_variant,p.Ile723Val,ENST00000324225,NM_001040455.1;SIDT2,missense_variant,p.Ile720Val,ENST00000431081,;SIDT2,missense_variant,p.Ile744Val,ENST00000278951,;SIDT2,missense_variant,p.Ile15Val,ENST00000532062,;SIDT2,missense_variant,p.Ile61Val,ENST00000525478,;SIDT2,downstream_gene_variant,,ENST00000525339,;SIDT2,non_coding_transcript_exon_variant,,ENST00000529484,;SIDT2,downstream_gene_variant,,ENST00000524988,;SIDT2,downstream_gene_variant,,ENST00000525065,;SIDT2,downstream_gene_variant,,ENST00000526813,;SIDT2,downstream_gene_variant,,ENST00000527654,;SIDT2,downstream_gene_variant,,ENST00000529441,;	G	ENSG00000149577	ENST00000324225	Transcript	missense_variant	2698/4406	2167/2499	723/832	I/V	Atc/Gtc	COSV54060557	1		1	SIDT2	HGNC	24272	protein_coding	YES	CCDS31682.1	ENSP00000314023	Q8NBJ9	G3V172,E9PPN9,E9PME7,E9PMC3	UPI000004BA68	NM_001040455.1	deleterious(0)	possibly_damaging(0.842)	23/26		Pfam:PF13965,PANTHER:PTHR12185,PANTHER:PTHR12185:SF16,Transmembrane_helices:TMhelix											1						MODERATE	1	SNV			1											.	CAT	.	.																					117063930
TMEM218	219854	.	GRCh37	11	124972208	124972208	+	5'UTR	SNP	A	A	G	rs14065		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.-71T>C			ENST00000455225	2/4	11	1	10	5	5	0	TMEM218,5_prime_UTR_variant,,ENST00000455225,;TMEM218,5_prime_UTR_variant,,ENST00000531909,NM_001080546.2,NM_001258246.1,NM_001258242.1,NM_001258243.1,NM_001258239.1;TMEM218,5_prime_UTR_variant,,ENST00000528724,;TMEM218,5_prime_UTR_variant,,ENST00000532407,;TMEM218,5_prime_UTR_variant,,ENST00000279968,;TMEM218,5_prime_UTR_variant,,ENST00000526175,;TMEM218,5_prime_UTR_variant,,ENST00000532156,;TMEM218,5_prime_UTR_variant,,ENST00000524373,;TMEM218,5_prime_UTR_variant,,ENST00000533273,;TMEM218,5_prime_UTR_variant,,ENST00000529583,;TMEM218,5_prime_UTR_variant,,ENST00000529609,;TMEM218,5_prime_UTR_variant,,ENST00000527271,;TMEM218,5_prime_UTR_variant,,ENST00000529530,;TMEM218,intron_variant,,ENST00000527766,;TMEM218,intron_variant,,ENST00000531262,;TMEM218,non_coding_transcript_exon_variant,,ENST00000527257,;TMEM218,non_coding_transcript_exon_variant,,ENST00000532717,;TMEM218,intron_variant,,ENST00000531851,;,regulatory_region_variant,,ENSR00001018877,;	G	ENSG00000150433	ENST00000455225	Transcript	5_prime_UTR_variant	582/2104					rs14065	1		-1	TMEM218	HGNC	27344	protein_coding	YES	CCDS31715.1	ENSP00000399803	A2RU14	E9PQM6,E9PL96	UPI00001617A4				2/4			0.7919	0.8979	0.6513		0.7817	0.7247	0.8282										MODIFIER	1	SNV														.	CAA	.	.												0.743	0.8758	0.6412	0.7952	0.8057	0.717	0.7228	0.7593	0.8068	124972208
PRB4	5545	.	GRCh37	12	11461706	11461706	+	Missense_Mutation	SNP	G	G	T	rs12308381		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.211C>A	p.Pro71Thr	p.P71T	ENST00000279575	3/4	483	356	127	273			PRB4,missense_variant,p.Pro71Thr,ENST00000279575,NM_001261399.1,NM_002723.4;PRB4,missense_variant,p.Pro71Thr,ENST00000535904,;PRB4,missense_variant,p.Pro71Thr,ENST00000445719,;	T	ENSG00000230657	ENST00000279575	Transcript	missense_variant	245/913	211/744	71/247	P/T	Ccc/Acc	rs12308381	1		-1	PRB4	HGNC	9340	protein_coding	YES	CCDS8641.1	ENSP00000279575		E9PAL0	UPI000013DBDC	NM_001261399.1,NM_002723.4	tolerated_low_confidence(0.25)	possibly_damaging(0.51)	3/4		Low_complexity_(Seg):seg,PANTHER:PTHR23203:SF4,PANTHER:PTHR23203,Pfam:PF15240,Prints:PR01217																	MODERATE	1	SNV														.	GGA	.	.												0.2248	0.3224	0.2081	0.08385	0.2421	0.3215	0.2352	0.1695	0.1532	11461706
CPNE8	144402	.	GRCh37	12	39155920	39155920	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.674A>G	p.Tyr225Cys	p.Y225C	ENST00000331366	9/20	234	225	9	165	165	0	CPNE8,missense_variant,p.Tyr225Cys,ENST00000331366,NM_153634.2;CPNE8,missense_variant,p.Tyr213Cys,ENST00000360449,;CPNE8,non_coding_transcript_exon_variant,,ENST00000551855,;,regulatory_region_variant,,ENSR00001547335,;	C	ENSG00000139117	ENST00000331366	Transcript	missense_variant	771/3489	674/1695	225/564	Y/C	tAt/tGt		1		-1	CPNE8	HGNC	23498	protein_coding	YES	CCDS8733.1	ENSP00000329748	Q86YQ8	Q86VY2	UPI000015FF59	NM_153634.2	deleterious(0.02)	probably_damaging(0.964)	9/20		Gene3D:2.60.40.150,Pfam:PF00168,PROSITE_profiles:PS50004,PANTHER:PTHR10857,PANTHER:PTHR10857:SF9,SMART:SM00239,Superfamily:SSF49562																	MODERATE	1	SNV														.	ATA	.	.																					39155920
ZNF740	283337	.	GRCh37	12	53581370	53581370	+	Missense_Mutation	SNP	T	T	C			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.578T>C	p.Leu193Pro	p.L193P	ENST00000416904	7/7	162	119	43	80	78	0	ZNF740,missense_variant,p.Leu193Pro,ENST00000416904,NM_001004304.3;ITGB7,downstream_gene_variant,,ENST00000267082,NM_000889.1;ITGB7,downstream_gene_variant,,ENST00000338737,;ITGB7,downstream_gene_variant,,ENST00000422257,;ITGB7,downstream_gene_variant,,ENST00000550743,;ITGB7,downstream_gene_variant,,ENST00000551319,;ZNF740,upstream_gene_variant,,ENST00000551514,;ITGB7,downstream_gene_variant,,ENST00000542497,;ZNF740,downstream_gene_variant,,ENST00000549739,;ZNF740,downstream_gene_variant,,ENST00000552593,;	C	ENSG00000139651	ENST00000416904	Transcript	missense_variant	1023/4249	578/582	193/193	L/P	cTa/cCa	COSV57240315	1		1	ZNF740	HGNC	27465	protein_coding	YES	CCDS44896.1	ENSP00000409463	Q8NDX6		UPI0000046CFF	NM_001004304.3	deleterious_low_confidence(0)	benign(0.144)	7/7		PANTHER:PTHR23229:SF93,PANTHER:PTHR23229											1						MODERATE	1	SNV			1											.	CTA	.	.																					53581370
CCT2	10576	.	GRCh37	12	69979115	69979115	+	5'UTR	SNP	G	G	C	rs2601007		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.-187G>C			ENST00000299300	1/16	14	8	6	4			CCT2,5_prime_UTR_variant,,ENST00000299300,NM_006431.2;CCT2,upstream_gene_variant,,ENST00000543146,NM_001198842.1;CCT2,upstream_gene_variant,,ENST00000544368,;MIR3913-1,upstream_gene_variant,,ENST00000577744,;CCT2,upstream_gene_variant,,ENST00000546850,;CCT2,upstream_gene_variant,,ENST00000546859,;CCT2,upstream_gene_variant,,ENST00000548787,;CCT2,upstream_gene_variant,,ENST00000549933,;CCT2,upstream_gene_variant,,ENST00000550010,;CCT2,upstream_gene_variant,,ENST00000550455,;CCT2,upstream_gene_variant,,ENST00000550638,;CCT2,upstream_gene_variant,,ENST00000551620,;CCT2,upstream_gene_variant,,ENST00000551899,;,regulatory_region_variant,,ENSR00000053778,;,TF_binding_site_variant,,ENSM00833036797,;	C	ENSG00000166226	ENST00000299300	Transcript	5_prime_UTR_variant	2/2041					rs2601007	1		1	CCT2	HGNC	1615	protein_coding	YES	CCDS8991.1	ENSP00000299300	P78371	Q9H369	UPI0000136AF3	NM_006431.2			1/16			0.4199	0.4932	0.4611		0.2708	0.329	0.5389										MODIFIER	1	SNV														.	AGT	.	.																					69979115
ANO4	121601	.	GRCh37	12	101490434	101490434	+	Intron	SNP	C	C	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1745+9C>T			ENST00000392979		188	143	45	133	132	0	ANO4,intron_variant,,ENST00000299222,;ANO4,intron_variant,,ENST00000392977,NM_001286615.1;ANO4,intron_variant,,ENST00000392979,NM_178826.3,NM_001286616.1;ANO4,intron_variant,,ENST00000550015,;	T	ENSG00000151572	ENST00000392979	Transcript	intron_variant							1		1	ANO4	HGNC	23837	protein_coding	YES	CCDS31884.1	ENSP00000376705	Q32M45		UPI0000198E2E	NM_178826.3,NM_001286616.1				18/26																		MODIFIER	1	SNV														.	CCT	.	.																					101490434
NT5DC3	51559	.	GRCh37	12	104181420	104181420	+	Intron	SNP	A	A	T	rs4964823		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1102-115T>A			ENST00000392876		12	6	6	6			NT5DC3,intron_variant,,ENST00000392876,NM_001031701.2;NT5DC3,intron_variant,,ENST00000474268,;NT5DC3,intron_variant,,ENST00000415849,;NT5DC3,upstream_gene_variant,,ENST00000447799,;	T	ENSG00000111696	ENST00000392876	Transcript	intron_variant						rs4964823	1		-1	NT5DC3	HGNC	30826	protein_coding	YES	CCDS41824.1	ENSP00000376615	Q86UY8		UPI0000192759	NM_001031701.2				10/13		0.3089	0.1029	0.3026		0.4583	0.2535	0.4949										MODIFIER	1	SNV														.	CAA	.	.																					104181420
HECTD4	283450	.	GRCh37	12	112622620	112622620	+	Missense_Mutation	SNP	C	C	T			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.9712G>A	p.Asp3238Asn	p.D3238N	ENST00000550722	61/76	168	131	37	61	59	0	HECTD4,missense_variant,p.Asp3238Asn,ENST00000550722,NM_001109662.3;HECTD4,missense_variant,p.Asp3212Asn,ENST00000377560,;HECTD4,missense_variant,p.Asp2962Asn,ENST00000430131,;	T	ENSG00000173064	ENST00000550722	Transcript	missense_variant	10108/15405	9712/12819	3238/4272	D/N	Gat/Aat	COSV66392154,COSV66401457	1		-1	HECTD4	HGNC	26611	protein_coding	YES		ENSP00000449784		F8VWT9,F8VU57	UPI00020CE513	NM_001109662.3	deleterious_low_confidence(0)	probably_damaging(0.982)	61/76		PANTHER:PTHR11254:SF286,PANTHER:PTHR11254											1,1						MODERATE	1	SNV			1,1											.	TCG	.	.																					112622620
SRRM4	84530	.	GRCh37	12	119554750	119554750	+	Missense_Mutation	SNP	C	C	A			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.374C>A	p.Ser125Tyr	p.S125Y	ENST00000267260	4/13	251	235	16	183	183	0	SRRM4,missense_variant,p.Ser125Tyr,ENST00000267260,NM_194286.3;RP11-364C11.2,non_coding_transcript_exon_variant,,ENST00000537730,;SRRM4,non_coding_transcript_exon_variant,,ENST00000545224,;	A	ENSG00000139767	ENST00000267260	Transcript	missense_variant	762/8477	374/1836	125/611	S/Y	tCc/tAc	COSV57421167	1		1	SRRM4	HGNC	29389	protein_coding	YES	CCDS44994.1	ENSP00000267260	A7MD48		UPI00001FBC3F	NM_194286.3	deleterious_low_confidence(0)	probably_damaging(0.997)	4/13		Low_complexity_(Seg):seg											1						MODERATE	1	SNV			1											.	TCC	.	.																					119554750
TMEM132B	114795	.	GRCh37	12	126136863	126136863	+	Intron	SNP	C	C	T	rs3825381		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1900-124C>T			ENST00000299308		13	7	6	7			TMEM132B,intron_variant,,ENST00000299308,NM_052907.2;TMEM132B,intron_variant,,ENST00000535886,NM_001286219.1;	T	ENSG00000139364	ENST00000299308	Transcript	intron_variant						rs3825381	1		1	TMEM132B	HGNC	29397	protein_coding	YES	CCDS41859.1	ENSP00000299308	Q14DG7		UPI00006BFF58	NM_052907.2				7/8		0.3401	0.4909	0.4496		0.2778	0.2505	0.2147										MODIFIER	1	SNV														.	CCG	.	.																					126136863
NEK5	341676	.	GRCh37	13	52684815	52684815	+	Intron	SNP	C	C	T	rs762964010		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.313-102G>A			ENST00000355568		48	38	10	92			NEK5,intron_variant,,ENST00000355568,NM_199289.1;NEK5,intron_variant,,ENST00000465811,;	T	ENSG00000197168	ENST00000355568	Transcript	intron_variant						rs762964010	1		-1	NEK5	HGNC	7748	protein_coding	YES	CCDS31979.1	ENSP00000347767	Q6P3R8		UPI0000227E77	NM_199289.1				5/21																		MODIFIER	1	SNV														.	ACA	.	.																					52684815
NEK5	341676	.	GRCh37	13	52684817	52684817	+	Intron	SNP	C	T	T	rs9535865		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.313-104G>A			ENST00000355568		46	8	38	91			NEK5,intron_variant,,ENST00000355568,NM_199289.1;NEK5,intron_variant,,ENST00000465811,;	T	ENSG00000197168	ENST00000355568	Transcript	intron_variant						rs9535865	1		-1	NEK5	HGNC	7748	protein_coding	YES	CCDS31979.1	ENSP00000347767	Q6P3R8		UPI0000227E77	NM_199289.1				5/21		0.0839	0.0166	0.1297			0.2535	0.0542										MODIFIER	1	SNV														.	ACA	.	.																					52684817
ABCC4	10257	.	GRCh37	13	95673941	95673941	+	Splice_Region	SNP	A	A	G	rs772961654		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.3871-5T>C			ENST00000376887		91	83	7	125	122	3	ABCC4,splice_region_variant,,ENST00000376887,NM_005845.3;ABCC4,splice_region_variant,,ENST00000412704,;RNU6-62P,downstream_gene_variant,,ENST00000516526,;	G	ENSG00000125257	ENST00000376887	Transcript	splice_region_variant,intron_variant						rs772961654	1		-1	ABCC4	HGNC	55	protein_coding	YES	CCDS9474.1	ENSP00000366084	O15439	Q8IUA3	UPI00001A36E6	NM_005845.3				30/30																		LOW	1	SNV														.	GAA	.	.												0.006449	0.002362	0.007884	0.007207	0.00523	0.004079	0.007759	0.007688	0.004339	95673941
COL4A2	1284	.	GRCh37	13	111164102	111164102	+	Intron	SNP	T	C	C	rs3742186		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.4882-179T>C			ENST00000360467		4	0	4	1			COL4A2,intron_variant,,ENST00000360467,NM_001846.2;COL4A2-AS1,upstream_gene_variant,,ENST00000417970,;COL4A2,intron_variant,,ENST00000463084,;COL4A2,downstream_gene_variant,,ENST00000480609,;,regulatory_region_variant,,ENSR00001063976,;,regulatory_region_variant,,ENSR00001564535,;,TF_binding_site_variant,,ENSM00899271369,;,TF_binding_site_variant,,ENSM00642374647,;	C	ENSG00000134871	ENST00000360467	Transcript	intron_variant						rs3742186	1		1	COL4A2	HGNC	2203	protein_coding	YES	CCDS41907.1	ENSP00000353654	P08572	A2A352	UPI000041C713	NM_001846.2				47/47		0.5006	0.5461	0.6095		0.3313	0.5765	0.4581										MODIFIER	1	SNV													1	.	ATG	.	.																					111164102
TMEM260	54916	.	GRCh37	14	57101581	57101581	+	Intron	SNP	T	T	G	rs777803225		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1725-36T>G			ENST00000261556		102	65	34	125	116	9	TMEM260,intron_variant,,ENST00000261556,NM_017799.3;TMEM260,intron_variant,,ENST00000536419,;TMEM260,intron_variant,,ENST00000538838,;TMEM260,upstream_gene_variant,,ENST00000555046,;RP11-1085N6.2,intron_variant,,ENST00000553800,;RP11-1085N6.2,intron_variant,,ENST00000555924,;TMEM260,intron_variant,,ENST00000539559,;TMEM260,intron_variant,,ENST00000555497,;TMEM260,intron_variant,,ENST00000556422,;TMEM260,intron_variant,,ENST00000556648,;TMEM260,downstream_gene_variant,,ENST00000555905,;	G	ENSG00000070269	ENST00000261556	Transcript	intron_variant						rs777803225	1		1	TMEM260	HGNC	20185	protein_coding	YES	CCDS9727.2	ENSP00000261556	Q9NX78	G3V4Y3,B3KN73	UPI00001FD5D2	NM_017799.3				13/15																		MODIFIER	1	SNV													1	.	GTG	.	.												0.003141	0.001253	0.0005231	0.0008716	0.0007554	0.0159	0.002828	0.003921	0.00218	57101581
TDRD9	122402	.	GRCh37	14	104431642	104431642	+	Intron	SNP	A	A	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.421-28A>T			ENST00000409874		41	29	12	49	49	0	TDRD9,intron_variant,,ENST00000339063,;TDRD9,intron_variant,,ENST00000409874,NM_153046.2;TDRD9,intron_variant,,ENST00000496087,;TDRD9,intron_variant,,ENST00000554571,;	T	ENSG00000156414	ENST00000409874	Transcript	intron_variant							1		1	TDRD9	HGNC	20122	protein_coding	YES	CCDS9987.2	ENSP00000387303	Q8NDG6		UPI0001642306	NM_153046.2				3/35																		MODIFIER	1	SNV													1	.	GAT	.	.																					104431642
GOLGA6L2	283685	.	GRCh37	15	23685920	23685920	+	Missense_Mutation	SNP	A	A	C	rs200451908		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1702T>G	p.Ser568Ala	p.S568A	ENST00000567107	8/8	32	26	5	30	30	0	GOLGA6L2,missense_variant,p.Ser568Ala,ENST00000567107,;GOLGA6L2,intron_variant,,ENST00000312015,;GOLGA6L2,intron_variant,,ENST00000345070,;GOLGA6L2,3_prime_UTR_variant,,ENST00000566571,;	C	ENSG00000174450	ENST00000567107	Transcript	missense_variant	1755/3030	1702/2730	568/909	S/A	Tca/Gca	rs200451908	1		-1	GOLGA6L2	HGNC	26695	protein_coding	YES		ENSP00000454407		H3BMJ4	UPI00024672CE		tolerated_low_confidence(0.21)	unknown(0)	8/8		Low_complexity_(Seg):seg																	MODERATE	1	SNV														.	GAT	.	.												6.76e-05	0.0007974	0.0002542		0.001068					23685920
GOLGA6L2	283685	.	GRCh37	15	23685922	23685922	+	Missense_Mutation	SNP	C	C	T	rs377626801		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.1700G>A	p.Gly567Glu	p.G567E	ENST00000567107	8/8	34	26	7	31	31	0	GOLGA6L2,missense_variant,p.Gly567Glu,ENST00000567107,;GOLGA6L2,intron_variant,,ENST00000312015,;GOLGA6L2,intron_variant,,ENST00000345070,;GOLGA6L2,3_prime_UTR_variant,,ENST00000566571,;	T	ENSG00000174450	ENST00000567107	Transcript	missense_variant	1753/3030	1700/2730	567/909	G/E	gGa/gAa	rs377626801,COSV61472904	1		-1	GOLGA6L2	HGNC	26695	protein_coding	YES		ENSP00000454407		H3BMJ4	UPI00024672CE		tolerated_low_confidence(0.1)	unknown(0)	8/8		Low_complexity_(Seg):seg											0,1						MODERATE	1	SNV			0,1											.	TCC	.	.																					23685922
TRIM69	140691	.	GRCh37	15	45028919	45028919	+	Intron	SNP	C	C	T	rs2468068		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.6+11C>T			ENST00000559390		231	219	10	155	154	0	TRIM69,intron_variant,,ENST00000329464,NM_182985.3;TRIM69,intron_variant,,ENST00000338264,;TRIM69,intron_variant,,ENST00000558329,;TRIM69,intron_variant,,ENST00000559390,;TRIM69,intron_variant,,ENST00000560442,NM_080745.3;TRIM69,intron_variant,,ENST00000561043,;TRIM69,downstream_gene_variant,,ENST00000559315,;TRIM69,downstream_gene_variant,,ENST00000560141,;TRIM69,downstream_gene_variant,,ENST00000560554,;	T	ENSG00000185880	ENST00000559390	Transcript	intron_variant						rs2468068	1		1	TRIM69	HGNC	17857	protein_coding	YES	CCDS32220.1	ENSP00000453177	Q86WT6		UPI0000246EB4					2/7																		MODIFIER	1	SNV														.	CCT	.	.												4.325e-05		0.0001065			5.923e-05	3.14e-05		7.976e-05	45028919
WDR72	256764	.	GRCh37	15	53907842	53907842	+	Missense_Mutation	SNP	A	A	T	rs757660889		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.2561T>A	p.Ile854Lys	p.I854K	ENST00000396328	15/20	77	57	20	106	106	0	WDR72,missense_variant,p.Ile854Lys,ENST00000396328,NM_182758.3,NM_001277176.1;WDR72,missense_variant,p.Ile851Lys,ENST00000557913,;WDR72,missense_variant,p.Ile854Lys,ENST00000360509,;WDR72,missense_variant,p.Ile864Lys,ENST00000559418,;WDR72,downstream_gene_variant,,ENST00000560036,;	T	ENSG00000166415	ENST00000396328	Transcript	missense_variant	2801/7507	2561/3309	854/1102	I/K	aTa/aAa	rs757660889,COSV64753642	1		-1	WDR72	HGNC	26790	protein_coding	YES	CCDS10151.1	ENSP00000379619	Q3MJ13	H0YN02	UPI00001D777D	NM_182758.3,NM_001277176.1	tolerated(0.57)	benign(0)	15/20		PANTHER:PTHR12816,PANTHER:PTHR12816:SF18											0,1						MODERATE	1	SNV			0,1										1	.	TAT	.	.												4.02e-06						8.916e-06			53907842
SNX1	6642	.	GRCh37	15	64415581	64415581	+	Intron	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.467-121G>T			ENST00000261889		138	133	5	124	124	0	SNX1,intron_variant,,ENST00000261889,NM_001242933.1,NM_003099.4;SNX1,intron_variant,,ENST00000353874,;SNX1,intron_variant,,ENST00000558040,;SNX1,intron_variant,,ENST00000559061,;SNX1,intron_variant,,ENST00000559844,;SNX1,intron_variant,,ENST00000560829,;SNX1,intron_variant,,ENST00000561026,NM_148955.3;SNX1,intron_variant,,ENST00000380285,;SNX1,intron_variant,,ENST00000559389,;SNX1,intron_variant,,ENST00000560260,;	T	ENSG00000028528	ENST00000261889	Transcript	intron_variant							1		1	SNX1	HGNC	11172	protein_coding	YES	CCDS58371.1	ENSP00000261889	Q13596	H0YKT3	UPI000217BDBB	NM_001242933.1,NM_003099.4				4/14																		MODIFIER	1	SNV														.	TGA	.	.																					64415581
KIAA1024	23251	.	GRCh37	15	79749365	79749365	+	Silent	SNP	G	G	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.876G>A	p.Lys292=	p.K292=	ENST00000305428	2/4	155	149	6	107	107	0	KIAA1024,synonymous_variant,p.Lys292=,ENST00000305428,NM_015206.2;KIAA1024,synonymous_variant,p.Lys292=,ENST00000559272,;	A	ENSG00000169330	ENST00000305428	Transcript	synonymous_variant	951/6732	876/2751	292/916	K	aaG/aaA		1		1	KIAA1024	HGNC	29172	protein_coding	YES	CCDS32306.1	ENSP00000307461	Q9UPX6		UPI00001B2F56	NM_015206.2			2/4		PANTHER:PTHR31530,PANTHER:PTHR31530:SF2																	LOW	1	SNV														.	AGG	.	.																					79749365
PIGQ	9091	.	GRCh37	16	626346	626346	+	Intron	SNP	A	A	C	rs2071980		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.942+92A>C			ENST00000026218		12	7	5	5			PIGQ,3_prime_UTR_variant,,ENST00000470411,;PIGQ,intron_variant,,ENST00000026218,NM_148920.2;PIGQ,intron_variant,,ENST00000321878,NM_004204.3;PIGQ,intron_variant,,ENST00000409527,;PIGQ,downstream_gene_variant,,ENST00000293874,;PIGQ,downstream_gene_variant,,ENST00000409439,;PIGQ,downstream_gene_variant,,ENST00000422307,;PIGQ,downstream_gene_variant,,ENST00000439574,;PIGQ,upstream_gene_variant,,ENST00000540241,;PIGQ,upstream_gene_variant,,ENST00000544860,;PIGQ,intron_variant,,ENST00000443147,;PIGQ,upstream_gene_variant,,ENST00000420990,;PIGQ,upstream_gene_variant,,ENST00000480424,;PIGQ,upstream_gene_variant,,ENST00000537901,;	C	ENSG00000007541	ENST00000026218	Transcript	intron_variant						rs2071980	1		1	PIGQ	HGNC	14135	protein_coding	YES	CCDS10411.1	ENSP00000026218	Q9BRB3	J3QTH6,B8ZZC7,B8ZZ31,B8ZZ29	UPI000006CC88	NM_148920.2				4/9		0.5339	0.4871	0.4914		0.6369	0.4334	0.6247										MODIFIER	1	SNV													1	.	CAC	.	.																					626346
RAB40C	57799	.	GRCh37	16	668443	668443	+	Intron	SNP	A	A	G	rs34011309		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.264+183A>G			ENST00000535977		5	1	4	8			RAB40C,intron_variant,,ENST00000248139,NM_021168.4;RAB40C,intron_variant,,ENST00000535977,NM_001172663.1;RAB40C,intron_variant,,ENST00000538492,NM_001172665.1,NM_001172666.1;RAB40C,intron_variant,,ENST00000539661,NM_001172664.1;RAB40C,intron_variant,,ENST00000563109,;RAB40C,intron_variant,,ENST00000564703,;RAB40C,intron_variant,,ENST00000566290,;RAB40C,intron_variant,,ENST00000568586,;RAB40C,intron_variant,,ENST00000569575,;RAB40C,intron_variant,,ENST00000509637,;RAB40C,intron_variant,,ENST00000565511,;	G	ENSG00000197562	ENST00000535977	Transcript	intron_variant						rs34011309	1		1	RAB40C	HGNC	18285	protein_coding	YES	CCDS10413.1	ENSP00000438492	Q96S21	Q5PXE8,H3BTC6,H3BNV8,H3BMH4,H3BME4	UPI0000133002	NM_001172663.1				4/6		0.5383	0.4985	0.4885		0.6488	0.4324	0.6227										MODIFIER	1	SNV														.	TAC	.	.																					668443
PKD1	5310	.	GRCh37	16	2153508	2153508	+	Silent	SNP	C	C	T	rs145648167		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.8550G>A	p.Ser2850=	p.S2850=	ENST00000262304	23/46	23	12	11	5			PKD1,synonymous_variant,p.Ser2850=,ENST00000262304,NM_001009944.2;PKD1,synonymous_variant,p.Ser2850=,ENST00000423118,NM_000296.3;PKD1,intron_variant,,ENST00000567946,;PKD1,downstream_gene_variant,,ENST00000483024,;PKD1,downstream_gene_variant,,ENST00000488185,;PKD1,non_coding_transcript_exon_variant,,ENST00000475889,;PKD1,downstream_gene_variant,,ENST00000473780,;PKD1,downstream_gene_variant,,ENST00000483558,;PKD1,downstream_gene_variant,,ENST00000561991,;PKD1,downstream_gene_variant,,ENST00000564865,;PKD1,upstream_gene_variant,,ENST00000566784,;PKD1,upstream_gene_variant,,ENST00000566905,;PKD1,upstream_gene_variant,,ENST00000570193,;PKD1,non_coding_transcript_exon_variant,,ENST00000486339,;PKD1,non_coding_transcript_exon_variant,,ENST00000496574,;PKD1,non_coding_transcript_exon_variant,,ENST00000483731,;PKD1,non_coding_transcript_exon_variant,,ENST00000415938,;PKD1,non_coding_transcript_exon_variant,,ENST00000471603,;PKD1,non_coding_transcript_exon_variant,,ENST00000480227,;PKD1,non_coding_transcript_exon_variant,,ENST00000562297,;PKD1,intron_variant,,ENST00000487932,;PKD1,upstream_gene_variant,,ENST00000469851,;PKD1,upstream_gene_variant,,ENST00000474088,;PKD1,upstream_gene_variant,,ENST00000483814,;PKD1,downstream_gene_variant,,ENST00000564890,;PKD1,downstream_gene_variant,,ENST00000565639,;PKD1,downstream_gene_variant,,ENST00000568591,;PKD1,downstream_gene_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000570253,;	T	ENSG00000008710	ENST00000262304	Transcript	synonymous_variant	8759/14138	8550/12912	2850/4303	S	tcG/tcA	rs145648167	1		-1	PKD1	HGNC	9008	protein_coding	YES	CCDS32369.1	ENSP00000262304	P98161	O75276	UPI00001B0454	NM_001009944.2			23/46		PANTHER:PTHR10877:SF123,PANTHER:PTHR10877	0.0002	0.0008							0.0002379								LOW	1	SNV													1	.	TCG	.	.												0.0003503	6.796e-05	0.0004637	0.00162	0.0001098	0.0003644	0.0003289	0.0006702	9.806e-05	2153508
IGHV3OR16-8	0	.	GRCh37	16	33020809	33020809	+	Missense_Mutation	SNP	G	G	A	rs201252363		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.217G>A	p.Asp73Asn	p.D73N	ENST00000565407	2/2	243	232	11	147	143	3	IGHV3OR16-8,missense_variant,p.Asp73Asn,ENST00000565407,;RP11-19N8.2,intron_variant,,ENST00000567619,;,regulatory_region_variant,,ENSR00000280452,;,regulatory_region_variant,,ENSR00001585911,;	A	ENSG00000271130	ENST00000565407	Transcript	missense_variant	217/349	217/349	73/116	D/N	Gat/Aat	rs201252363	1		1	IGHV3OR16-8	HGNC	5643	IG_V_gene	YES		ENSP00000474964			UPI00033351ED		tolerated_low_confidence(0.43)	benign(0)	2/2		Gene3D:2.60.40.10,Pfam:PF07686,PROSITE_profiles:PS50835,PANTHER:PTHR23266,PANTHER:PTHR23266:SF80,SMART:SM00406,Superfamily:SSF48726																	MODERATE	1	SNV														.	TGA	.	.												0.0006938	0.001508	8.955e-05	0.0003126	0.001915	0.0003953	0.0004937	0.0005278	0.00142	33020809
MYO1C	4641	.	GRCh37	17	1382576	1382576	+	Intron	SNP	G	G	C	rs8076825		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.1092+149C>G			ENST00000359786		8	3	5	4			MYO1C,intron_variant,,ENST00000359786,NM_001080779.1;MYO1C,intron_variant,,ENST00000361007,NM_033375.4;MYO1C,intron_variant,,ENST00000438665,NM_001080950.1;MYO1C,intron_variant,,ENST00000545534,;MYO1C,intron_variant,,ENST00000575158,;MYO1C,downstream_gene_variant,,ENST00000570490,;MYO1C,downstream_gene_variant,,ENST00000570984,;MYO1C,downstream_gene_variant,,ENST00000571715,;MYO1C,downstream_gene_variant,,ENST00000573853,;MYO1C,downstream_gene_variant,,ENST00000574790,;MYO1C,downstream_gene_variant,,ENST00000575335,;MYO1C,intron_variant,,ENST00000573198,;MYO1C,downstream_gene_variant,,ENST00000571851,;MYO1C,downstream_gene_variant,,ENST00000576822,;MYO1C,upstream_gene_variant,,ENST00000571615,;MYO1C,upstream_gene_variant,,ENST00000573961,;	C	ENSG00000197879	ENST00000359786	Transcript	intron_variant						rs8076825	1		-1	MYO1C	HGNC	7597	protein_coding	YES	CCDS42226.1	ENSP00000352834	O00159	I3L4D4,I3L3Y6,I3L3F5,I3L204,I3L168	UPI0000200579	NM_001080779.1				9/31		0.3630	0.5734	0.3386		0.2371	0.3002	0.2904										MODIFIER	1	SNV													1	.	CGG	.	.																					1382576
CHD3	1107	.	GRCh37	17	7803016	7803016	+	Intron	SNP	T	T	G	rs1035903262		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.2721+155T>G			ENST00000380358		18	14	4	22	0	0	CHD3,intron_variant,,ENST00000330494,NM_001005273.2;CHD3,intron_variant,,ENST00000358181,NM_005852.3;CHD3,intron_variant,,ENST00000380358,NM_001005271.2;CHD3,downstream_gene_variant,,ENST00000452447,;CHD3,upstream_gene_variant,,ENST00000466233,;CHD3,upstream_gene_variant,,ENST00000470531,;CHD3,upstream_gene_variant,,ENST00000473376,;CHD3,downstream_gene_variant,,ENST00000479080,;CHD3,downstream_gene_variant,,ENST00000572579,;	G	ENSG00000170004	ENST00000380358	Transcript	intron_variant						rs1035903262	1		1	CHD3	HGNC	1918	protein_coding	YES	CCDS32553.2	ENSP00000369716	Q12873	Q2TAZ1	UPI00004DDA7C	NM_001005271.2				15/39																		MODIFIER	1	SNV													1	.	GTA	.	.																					7803016
SLFN14	342618	.	GRCh37	17	33884688	33884688	+	Missense_Mutation	SNP	G	G	A	rs199663871		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.394C>T	p.Arg132Trp	p.R132W	ENST00000415846	1/4	62	45	17	71	71	0	SLFN14,missense_variant,p.Arg132Trp,ENST00000415846,NM_001129820.1;RP11-1094M14.14,downstream_gene_variant,,ENST00000591634,;RP11-1094M14.12,downstream_gene_variant,,ENST00000588445,;	A	ENSG00000236320	ENST00000415846	Transcript	missense_variant	430/2889	394/2739	132/912	R/W	Cgg/Tgg	rs199663871,COSV70570630	1		-1	SLFN14	HGNC	32689	protein_coding	YES	CCDS45650.1	ENSP00000391101	P0C7P3		UPI000041A9FB	NM_001129820.1	tolerated(0.1)	benign(0.153)	1/4		PANTHER:PTHR12155,PANTHER:PTHR12155:SF22	0.0004					0.001	0.001				0,1						MODERATE	1	SNV			0,1										1	.	CGA	.	.												0.00104	0.0005066	0.0002025			0.0003928	0.002251		0.000483	33884688
STAT3	6774	.	GRCh37	17	40489339	40489339	+	Intron	SNP	A	A	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.797+114T>G			ENST00000264657		17	10	7	15	15	0	STAT3,intron_variant,,ENST00000264657,NM_139276.2,NM_003150.3;STAT3,intron_variant,,ENST00000389272,;STAT3,intron_variant,,ENST00000404395,;STAT3,intron_variant,,ENST00000585517,NM_213662.1;STAT3,intron_variant,,ENST00000588969,;,regulatory_region_variant,,ENSR00001127862,;	C	ENSG00000168610	ENST00000264657	Transcript	intron_variant							1		-1	STAT3	HGNC	11364	protein_coding	YES	CCDS32656.1	ENSP00000264657	P40763	G8JLH9	UPI0000031047	NM_139276.2,NM_003150.3				8/23																		MODIFIER	1	SNV													1	.	AAT	.	.																					40489339
STAT3	6774	.	GRCh37	17	40500265	40500265	+	Intron	SNP	C	C	A	rs2306581		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.128+142G>T			ENST00000264657		10	4	6	4			STAT3,intron_variant,,ENST00000264657,NM_139276.2,NM_003150.3;STAT3,intron_variant,,ENST00000389272,;STAT3,intron_variant,,ENST00000404395,;STAT3,intron_variant,,ENST00000585517,NM_213662.1;STAT3,intron_variant,,ENST00000588065,;STAT3,intron_variant,,ENST00000588969,;STAT3,intron_variant,,ENST00000585360,;,regulatory_region_variant,,ENSR00001127864,;	A	ENSG00000168610	ENST00000264657	Transcript	intron_variant						rs2306581	1		-1	STAT3	HGNC	11364	protein_coding	YES	CCDS32656.1	ENSP00000264657	P40763	G8JLH9	UPI0000031047	NM_139276.2,NM_003150.3				2/23			0.885	0.281		0.3988	0.3688	0.4908					24058746,15935090,18841165,28366820					MODIFIER	1	SNV													1	.	CCC	.	.																					40500265
FAM134C	162427	.	GRCh37	17	40737071	40737071	+	Intron	SNP	A	A	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.727+72T>C			ENST00000309428		58	45	13	41	41	0	FAM134C,intron_variant,,ENST00000309428,NM_178126.3;FAM134C,intron_variant,,ENST00000543197,;FAM134C,intron_variant,,ENST00000585894,;FAM134C,downstream_gene_variant,,ENST00000588423,;FAM134C,downstream_gene_variant,,ENST00000591547,;FAM134C,intron_variant,,ENST00000586870,;FAM134C,intron_variant,,ENST00000589007,;FAM134C,intron_variant,,ENST00000589797,;FAM134C,downstream_gene_variant,,ENST00000585726,;FAM134C,downstream_gene_variant,,ENST00000586796,;FAM134C,downstream_gene_variant,,ENST00000590035,;FAM134C,downstream_gene_variant,,ENST00000593251,;,regulatory_region_variant,,ENSR00001127923,;	G	ENSG00000141699	ENST00000309428	Transcript	intron_variant							1		-1	FAM134C	HGNC	27258	protein_coding	YES	CCDS11432.1	ENSP00000309432	Q86VR2	K7EQI9,K7ENZ6,K7EJ42,B3KR75	UPI0000171C73	NM_178126.3				6/8																		MODIFIER	1	SNV														.	TAT	.	.																					40737071
EFCAB13	124989	.	GRCh37	17	45456770	45456770	+	Intron	SNP	T	T	G	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1582+151T>G			ENST00000331493		19	15	4	31	31	0	EFCAB13,intron_variant,,ENST00000331493,NM_152347.4;EFCAB13,intron_variant,,ENST00000517484,NM_001195192.1;EFCAB13,intron_variant,,ENST00000523842,;EFCAB13,downstream_gene_variant,,ENST00000517310,;EFCAB13,downstream_gene_variant,,ENST00000523978,;EFCAB13,intron_variant,,ENST00000520776,;EFCAB13,intron_variant,,ENST00000522326,;	G	ENSG00000178852	ENST00000331493	Transcript	intron_variant							1		1	EFCAB13	HGNC	26864	protein_coding	YES	CCDS11512.1	ENSP00000332111	Q8IY85	E5RI18,E5RFW6	UPI00001AFEA2	NM_152347.4				14/24																		MODIFIER	1	SNV														.	CTA	.	.																					45456770
MRPL27	51264	.	GRCh37	17	48447481	48447481	+	Intron	SNP	G	G	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.173-21C>A			ENST00000225969		78	74	4	70	70	0	MRPL27,intron_variant,,ENST00000225969,NM_016504.2;MRPL27,intron_variant,,ENST00000442592,;MRPL27,intron_variant,,ENST00000503633,;MRPL27,intron_variant,,ENST00000507088,;MRPL27,intron_variant,,ENST00000508200,;MRPL27,intron_variant,,ENST00000511860,;EME1,upstream_gene_variant,,ENST00000338165,NM_152463.2;EME1,upstream_gene_variant,,ENST00000393271,NM_001166131.1;LRRC59,downstream_gene_variant,,ENST00000503118,;EME1,upstream_gene_variant,,ENST00000511519,;EME1,upstream_gene_variant,,ENST00000510007,;EME1,upstream_gene_variant,,ENST00000511711,;MRPL27,downstream_gene_variant,,ENST00000514928,;	T	ENSG00000108826	ENST00000225969	Transcript	intron_variant							1		-1	MRPL27	HGNC	14483	protein_coding	YES	CCDS11564.1	ENSP00000225969	Q9P0M9	D6RAN8	UPI00001342E1	NM_016504.2				2/3																		MODIFIER	1	SNV														.	TGA	.	.																					48447481
PPM1E	22843	.	GRCh37	17	56833491	56833491	+	Missense_Mutation	SNP	T	T	C	rs58091258		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.133T>C	p.Ser45Pro	p.S45P	ENST00000308249	1/7	45	34	11	13			PPM1E,missense_variant,p.Ser45Pro,ENST00000308249,NM_014906.4;,regulatory_region_variant,,ENSR00000096303,;	C	ENSG00000175175	ENST00000308249	Transcript	missense_variant	262/2988	133/2268	45/755	S/P	Tcc/Ccc	rs58091258,COSV57575728	1		1	PPM1E	HGNC	19322	protein_coding	YES	CCDS11613.1	ENSP00000312411	Q8WY54	A7E2X1	UPI000013ECF6	NM_014906.4	tolerated_low_confidence(1)	benign(0)	1/7		Low_complexity_(Seg):seg,PANTHER:PTHR13832,PANTHER:PTHR13832:SF225	0.0070	0.0129	0.0029		0.0069	0.001	0.0082				0,1						MODERATE	1	SNV			0,1											.	GTC	.	.												0.0001041	0.0003045	9.401e-05				9.349e-05	0.000363	0.0001755	56833491
GRIN2C	2905	.	GRCh37	17	72838649	72838649	+	Missense_Mutation	SNP	C	C	A	rs3744215		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.3627G>T	p.Arg1209Ser	p.R1209S	ENST00000293190	13/13	18	8	10	7			GRIN2C,missense_variant,p.Arg1209Ser,ENST00000293190,NM_000835.4;TMEM104,downstream_gene_variant,,ENST00000335464,NM_017728.3;GRIN2C,downstream_gene_variant,,ENST00000347612,NM_001278553.1;TMEM104,downstream_gene_variant,,ENST00000417024,;TMEM104,downstream_gene_variant,,ENST00000582330,;TMEM104,downstream_gene_variant,,ENST00000582773,;TMEM104,downstream_gene_variant,,ENST00000584171,;GRIN2C,downstream_gene_variant,,ENST00000584176,;,regulatory_region_variant,,ENSR00000377800,;	A	ENSG00000161509	ENST00000293190	Transcript	missense_variant	3774/4261	3627/3702	1209/1233	R/S	agG/agT	rs3744215	1		-1	GRIN2C	HGNC	4587	protein_coding	YES	CCDS32724.1	ENSP00000293190	Q14957		UPI00001AEBA4	NM_000835.4	tolerated_low_confidence(0.08)	benign(0)	13/13			0.2895	0.2852	0.1931		0.381	0.2942	0.2648	0.3078	0.2831			23408766,26819771,16537520,31477688					MODERATE	1	SNV														.	CCC	.	.												0.2805	0.3048	0.1694	0.3801	0.4204	0.2947	0.2776	0.2803	0.2773	72838649
C18orf54	162681	.	GRCh37	18	51889346	51889346	+	Intron	SNP	C	C	A	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.740+55C>A			ENST00000300091		49	45	4	47	47	0	C18orf54,intron_variant,,ENST00000300091,NM_173529.4;C18orf54,intron_variant,,ENST00000382911,;C18orf54,intron_variant,,ENST00000578138,;C18orf54,upstream_gene_variant,,ENST00000582188,;	A	ENSG00000166845	ENST00000300091	Transcript	intron_variant							1		1	C18orf54	HGNC	13796	protein_coding	YES	CCDS11956.1	ENSP00000300091	Q8IYD9	J3KS56,J3KRX3,I7HAS0,I7GY12	UPI0000074279	NM_173529.4				4/7																		MODIFIER	1	SNV														.	GCG	.	.																					51889346
GZMM	3004	.	GRCh37	19	547491	547491	+	Intron	SNP	C	C	T	rs2070795		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.212+55C>T			ENST00000264553		6	1	5	8	8	0	GZMM,intron_variant,,ENST00000264553,NM_001258351.1,NM_005317.3;GZMM,intron_variant,,ENST00000592501,;	T	ENSG00000197540	ENST00000264553	Transcript	intron_variant						rs2070795	1		1	GZMM	HGNC	4712	protein_coding	YES	CCDS12031.1	ENSP00000264553	P51124		UPI000013D531	NM_001258351.1,NM_005317.3				2/4		0.4571	0.1936	0.5706		0.5615	0.7187	0.3558										MODIFIER	1	SNV														.	CCC	.	.																					547491
PLIN4	729359	.	GRCh37	19	4511350	4511350	+	Missense_Mutation	SNP	T	A	A	rs7259721		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.2580A>T	p.Lys860Asn	p.K860N	ENST00000301286	3/6	151	28	123	140			PLIN4,missense_variant,p.Lys860Asn,ENST00000301286,NM_001080400.1;	A	ENSG00000167676	ENST00000301286	Transcript	missense_variant	2580/6341	2580/4074	860/1357	K/N	aaA/aaT	rs7259721	1		-1	PLIN4	HGNC	29393	protein_coding	YES	CCDS45927.1	ENSP00000301286	Q96Q06	B4DHR7	UPI00001D822A	NM_001080400.1	tolerated(1)	benign(0)	3/6		Low_complexity_(Seg):seg,PANTHER:PTHR14024:SF24,PANTHER:PTHR14024																	MODERATE	1	SNV														.	CTT	.	.																					4511350
VAV1	7409	.	GRCh37	19	6836885	6836885	+	Intron	SNP	A	A	G	rs112275266		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1915-111A>G			ENST00000602142		32	6	26	10			VAV1,intron_variant,,ENST00000304076,NM_001258206.1;VAV1,intron_variant,,ENST00000539284,;VAV1,intron_variant,,ENST00000596764,NM_001258207.1;VAV1,intron_variant,,ENST00000599806,;VAV1,intron_variant,,ENST00000602142,NM_005428.3;VAV1,intron_variant,,ENST00000598270,;VAV1,downstream_gene_variant,,ENST00000597967,;VAV1,downstream_gene_variant,,ENST00000600396,;VAV1,downstream_gene_variant,,ENST00000601452,;	G	ENSG00000141968	ENST00000602142	Transcript	intron_variant						rs112275266	1		1	VAV1	HGNC	12657	protein_coding	YES	CCDS12174.1	ENSP00000472929	P15498		UPI0000138213	NM_005428.3				20/26		0.1613	0.5545	0.0504		0.002	0.0119	0.0266										MODIFIER	1	SNV													1	.	CAC	.	.																					6836885
EIF3G	8666	.	GRCh37	19	10226187	10226187	+	Silent	SNP	G	G	A	rs144649796		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.915C>T	p.Tyr305=	p.Y305=	ENST00000253108	10/11	95	64	31	72	70	1	EIF3G,synonymous_variant,p.Tyr305=,ENST00000253108,NM_003755.3;EIF3G,synonymous_variant,p.Tyr103=,ENST00000593054,;PPAN,downstream_gene_variant,,ENST00000253107,NM_020230.5;P2RY11,downstream_gene_variant,,ENST00000321826,NM_002566.4;PPAN,downstream_gene_variant,,ENST00000393793,;PPAN-P2RY11,downstream_gene_variant,,ENST00000393796,;PPAN-P2RY11,downstream_gene_variant,,ENST00000428358,NM_001198690.1,NM_001040664.2;PPAN,downstream_gene_variant,,ENST00000444703,;PPAN,downstream_gene_variant,,ENST00000556468,;EIF3G,downstream_gene_variant,,ENST00000587146,;EIF3G,downstream_gene_variant,,ENST00000588709,;EIF3G,downstream_gene_variant,,ENST00000589454,;P2RY11,downstream_gene_variant,,ENST00000471843,;EIF3G,downstream_gene_variant,,ENST00000587168,;EIF3G,non_coding_transcript_exon_variant,,ENST00000590158,;PPAN,downstream_gene_variant,,ENST00000468881,;PPAN,downstream_gene_variant,,ENST00000486482,;EIF3G,downstream_gene_variant,,ENST00000586151,;EIF3G,downstream_gene_variant,,ENST00000587590,;EIF3G,downstream_gene_variant,,ENST00000587681,;EIF3G,downstream_gene_variant,,ENST00000587993,;EIF3G,downstream_gene_variant,,ENST00000589009,;EIF3G,downstream_gene_variant,,ENST00000589458,;EIF3G,downstream_gene_variant,,ENST00000589674,;EIF3G,downstream_gene_variant,,ENST00000590647,;EIF3G,downstream_gene_variant,,ENST00000590940,;EIF3G,downstream_gene_variant,,ENST00000592485,;EIF3G,downstream_gene_variant,,ENST00000593066,;EIF3G,downstream_gene_variant,,ENST00000593095,;	A	ENSG00000130811	ENST00000253108	Transcript	synonymous_variant	958/1103	915/963	305/320	Y	taC/taT	rs144649796	1		-1	EIF3G	HGNC	3274	protein_coding	YES	CCDS12227.1	ENSP00000253108	O75821		UPI000012D2FE	NM_003755.3			10/11		HAMAP:MF_03006,PROSITE_profiles:PS50102,PANTHER:PTHR10352,Gene3D:3.30.70.330,PIRSF:PIRSF037949,SMART:SM00360,Superfamily:SSF54928									0.0001163								LOW	1	SNV														.	CGT	.	.												1.597e-05		2.898e-05				1.766e-05		3.283e-05	10226187
SYDE1	85360	.	GRCh37	19	15223466	15223466	+	Intron	SNP	A	A	G	rs4808977		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1804+84A>G			ENST00000342784		9	2	7	5			SYDE1,intron_variant,,ENST00000342784,NM_033025.4;SYDE1,intron_variant,,ENST00000600252,;SYDE1,intron_variant,,ENST00000600440,;SYDE1,intron_variant,,ENST00000602203,;ILVBL,downstream_gene_variant,,ENST00000263383,NM_006844.4;ILVBL,downstream_gene_variant,,ENST00000534378,;SYDE1,downstream_gene_variant,,ENST00000597977,;ILVBL,downstream_gene_variant,,ENST00000598709,;ILVBL,downstream_gene_variant,,ENST00000524779,;ILVBL,downstream_gene_variant,,ENST00000525880,;ILVBL,downstream_gene_variant,,ENST00000533086,;ILVBL,downstream_gene_variant,,ENST00000533148,;ILVBL,downstream_gene_variant,,ENST00000534806,;ILVBL,downstream_gene_variant,,ENST00000596093,;,regulatory_region_variant,,ENSR00001156923,;,regulatory_region_variant,,ENSR00001609932,;,TF_binding_site_variant,,ENSM00527326978,;	G	ENSG00000105137	ENST00000342784	Transcript	intron_variant						rs4808977	1		1	SYDE1	HGNC	25824	protein_coding	YES	CCDS12324.1	ENSP00000341489	Q6ZW31		UPI00001C092C	NM_033025.4				7/7		0.9129	0.879	0.9496		0.8681	0.9642	0.9264										MODIFIER	1	SNV														.	TAG	.	.																					15223466
CPAMD8	27151	.	GRCh37	19	17008578	17008578	+	Silent	SNP	G	G	C	rs2608732		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.5130C>G	p.Thr1710=	p.T1710=	ENST00000443236	39/42	85	52	33	13	12	1	CPAMD8,synonymous_variant,p.Thr1710=,ENST00000443236,NM_015692.2;CPAMD8,synonymous_variant,p.Thr186=,ENST00000594249,;CPAMD8,synonymous_variant,p.Thr72=,ENST00000599287,;CPAMD8,upstream_gene_variant,,ENST00000598792,;CPAMD8,upstream_gene_variant,,ENST00000595323,;CPAMD8,upstream_gene_variant,,ENST00000597335,;CPAMD8,upstream_gene_variant,,ENST00000598547,;CPAMD8,upstream_gene_variant,,ENST00000602132,;CPAMD8,non_coding_transcript_exon_variant,,ENST00000601782,;CPAMD8,non_coding_transcript_exon_variant,,ENST00000597709,;CPAMD8,upstream_gene_variant,,ENST00000593739,;CPAMD8,upstream_gene_variant,,ENST00000596224,;CPAMD8,upstream_gene_variant,,ENST00000596572,;CPAMD8,upstream_gene_variant,,ENST00000598104,;CPAMD8,upstream_gene_variant,,ENST00000600235,;,regulatory_region_variant,,ENSR00000107818,;,TF_binding_site_variant,,ENSM00526027801,;	C	ENSG00000160111	ENST00000443236	Transcript	synonymous_variant	5162/5992	5130/5799	1710/1932	T	acC/acG	rs2608732	1		-1	CPAMD8	HGNC	23228	protein_coding	YES	CCDS42519.1	ENSP00000402505	Q8IZJ3		UPI0000E8AC99	NM_015692.2			39/42		PANTHER:PTHR11412:SF76,PANTHER:PTHR11412,Superfamily:SSF49410	0.5649	0.8064	0.5879		0.3016	0.5368	0.5225	0.7611	0.5335			29149250					LOW	1	SNV													1	.	GGG	.	.												0.5147	0.7546	0.5071	0.5586	0.3089	0.5417	0.5048	0.5405	0.5386	17008578
CCNE1	898	.	GRCh37	19	30312915	30312915	+	Missense_Mutation	SNP	C	C	T	rs1411284279		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.718C>T	p.Arg240Cys	p.R240C	ENST00000262643	9/12	317	310	7	245	245	0	CCNE1,missense_variant,p.Arg240Cys,ENST00000262643,NM_001238.2;CCNE1,missense_variant,p.Arg197Cys,ENST00000357943,;CCNE1,missense_variant,p.Arg225Cys,ENST00000444983,;CCNE1,intron_variant,,ENST00000576532,;CCNE1,downstream_gene_variant,,ENST00000575243,;CCNE1,non_coding_transcript_exon_variant,,ENST00000574121,;	T	ENSG00000105173	ENST00000262643	Transcript	missense_variant	997/2043	718/1233	240/410	R/C	Cgt/Tgt	rs1411284279,COSV52904723	1		1	CCNE1	HGNC	1589	protein_coding	YES	CCDS12419.1	ENSP00000262643	P24864	F6KX26	UPI0000001C33	NM_001238.2	tolerated(0.07)	benign(0.006)	9/12		Superfamily:SSF47954,PIRSF:PIRSF001771,Pfam:PF00134,Gene3D:1.10.472.10,PANTHER:PTHR10177:SF71,PANTHER:PTHR10177											0,1						MODERATE	1	SNV			0,1										1	.	GCG	.	.												8.057e-06				5.495e-05		8.865e-06			30312915
CAPN12	147968	.	GRCh37	19	39227128	39227128	+	Intron	SNP	G	G	T	rs148871822		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.1374+64C>A			ENST00000328867		35	23	11	20			CAPN12,intron_variant,,ENST00000328867,NM_144691.3;CAPN12,intron_variant,,ENST00000601953,;ACTN4,downstream_gene_variant,,ENST00000252699,NM_004924.4;ACTN4,downstream_gene_variant,,ENST00000440400,;CAPN12,upstream_gene_variant,,ENST00000595177,;CAPN12,upstream_gene_variant,,ENST00000597987,;CTD-2540F13.2,upstream_gene_variant,,ENST00000602255,;CAPN12,intron_variant,,ENST00000597716,;CAPN12,upstream_gene_variant,,ENST00000593700,;CAPN12,upstream_gene_variant,,ENST00000594497,;CAPN12,upstream_gene_variant,,ENST00000594552,;CAPN12,upstream_gene_variant,,ENST00000597354,;CAPN12,upstream_gene_variant,,ENST00000601685,;,regulatory_region_variant,,ENSR00000109316,;	T	ENSG00000182472	ENST00000328867	Transcript	intron_variant						rs148871822	1		-1	CAPN12	HGNC	13249	protein_coding	YES	CCDS12519.1	ENSP00000331636	Q6ZSI9	M0R3D7	UPI00001C0E17	NM_144691.3				11/20		0.0028	0.0076	0.0014		0.002	0.001											MODIFIER	1	SNV														.	GGT	.	.																					39227128
CYP2A6	1548	.	GRCh37	19	41355849	41355849	+	Silent	SNP	A	A	G	rs2302990		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.217T>C	p.Leu73=	p.L73=	ENST00000301141	2/9	181	158	22	67	64	1	CYP2A6,synonymous_variant,p.Leu73=,ENST00000301141,NM_000762.5;CYP2A6,3_prime_UTR_variant,,ENST00000600495,;CYP2A6,intron_variant,,ENST00000596719,;CTC-490E21.12,intron_variant,,ENST00000601627,;	G	ENSG00000255974	ENST00000301141	Transcript	synonymous_variant	238/1764	217/1485	73/494	L	Ttg/Ctg	rs2302990	1		-1	CYP2A6	HGNC	2610	protein_coding	YES	CCDS12568.1	ENSP00000301141	P11509		UPI000013E6D2	NM_000762.5			2/9		Gene3D:1.10.630.10,Pfam:PF00067,Prints:PR00463,PANTHER:PTHR24300,PANTHER:PTHR24300:SF96,Superfamily:SSF48264																	LOW	1	SNV													1	.	AAG	.	.												0.003788	0.001681	0.00637	0.006972	0.002334	0.01117	0.002271	0.00373	0.002683	41355849
CYP2G1P	22952	.	GRCh37	19	41399887	41399887	+	RNA	SNP	A	A	G	rs12609982		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																n.1636A>G			ENST00000252909	2/5	12	3	9	3			CYP2G1P,non_coding_transcript_exon_variant,,ENST00000252909,;CTC-490E21.12,3_prime_UTR_variant,,ENST00000601627,;CYP2G1P,non_coding_transcript_exon_variant,,ENST00000597833,;	G	ENSG00000130612	ENST00000252909	Transcript	non_coding_transcript_exon_variant	1636/2511					rs12609982	1		1	CYP2G1P	HGNC	2633	processed_transcript	YES									2/5			0.1170	0.0862	0.0793		0.1915	0.1431	0.0818										MODIFIER		SNV														.	CAG	.	.																					41399887
LIG1	3978	.	GRCh37	19	48640625	48640625	+	Intron	SNP	A	A	C	rs419664		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.1254+154T>G			ENST00000263274		13	6	7	4			LIG1,intron_variant,,ENST00000263274,NM_000234.1;LIG1,intron_variant,,ENST00000427526,;LIG1,intron_variant,,ENST00000536218,;LIG1,intron_variant,,ENST00000542460,;LIG1,intron_variant,,ENST00000594067,;LIG1,intron_variant,,ENST00000594759,;LIG1,intron_variant,,ENST00000597901,;LIG1,intron_variant,,ENST00000601091,;LIG1,upstream_gene_variant,,ENST00000596457,;LIG1,upstream_gene_variant,,ENST00000596672,;	C	ENSG00000105486	ENST00000263274	Transcript	intron_variant						rs419664	1		-1	LIG1	HGNC	6598	protein_coding	YES	CCDS12711.1	ENSP00000263274	P18858	Q76GR4,M0R1S4,M0QY71	UPI0000129656	NM_000234.1				13/27			0.8918	0.5735		0.875	0.5616	0.5879										MODIFIER	1	SNV														.	GAT	.	.																					48640625
KLK15	55554	.	GRCh37	19	51329938	51329938	+	Missense_Mutation	SNP	C	C	T			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.557G>A	p.Gly186Glu	p.G186E	ENST00000598239	4/5	154	119	35	88	85	0	KLK15,missense_variant,p.Gly185Glu,ENST00000326856,;KLK15,missense_variant,p.Gly186Glu,ENST00000598239,NM_001277081.1,NM_017509.3;KLK15,intron_variant,,ENST00000301421,NM_001277082.1;KLK15,intron_variant,,ENST00000416184,;KLK15,intron_variant,,ENST00000596931,;KLK1,upstream_gene_variant,,ENST00000301420,NM_002257.3;KLK1,upstream_gene_variant,,ENST00000448701,;KLK15,downstream_gene_variant,,ENST00000598673,;AC011523.2,upstream_gene_variant,,ENST00000598079,;KLK15,3_prime_UTR_variant,,ENST00000602114,;KLK15,non_coding_transcript_exon_variant,,ENST00000596531,;KLK15,non_coding_transcript_exon_variant,,ENST00000601680,;KLK1,upstream_gene_variant,,ENST00000593325,;KLK1,upstream_gene_variant,,ENST00000593859,;	T	ENSG00000174562	ENST00000598239	Transcript	missense_variant	588/855	557/771	186/256	G/E	gGg/gAg	COSV56828457	1		-1	KLK15	HGNC	20453	protein_coding	YES	CCDS12805.1	ENSP00000469315	Q9H2R5	S5TEP0,M0R2F7	UPI000004CA04	NM_001277081.1,NM_017509.3	deleterious(0.02)	probably_damaging(0.998)	4/5		PROSITE_profiles:PS50240,PANTHER:PTHR24259,PANTHER:PTHR24259:SF68,Pfam:PF00089,Gene3D:2.40.10.10,SMART:SM00020,Superfamily:SSF50494											1						MODERATE	1	SNV			1											.	CCC	.	.																					51329938
KLK4	9622	.	GRCh37	19	51412500	51412500	+	Splice_Region	SNP	G	G	C	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.224+8C>G			ENST00000324041		69	58	11	25	25	0	KLK4,splice_region_variant,,ENST00000324041,NM_004917.3;KLK4,splice_region_variant,,ENST00000431178,;KLK4,upstream_gene_variant,,ENST00000597441,;KLK4,splice_region_variant,,ENST00000599865,;KLK4,5_prime_UTR_variant,,ENST00000598305,;KLK4,3_prime_UTR_variant,,ENST00000602148,;KLK4,non_coding_transcript_exon_variant,,ENST00000596876,;KLK4,upstream_gene_variant,,ENST00000593885,;,regulatory_region_variant,,ENSR00001164196,;	C	ENSG00000167749	ENST00000324041	Transcript	splice_region_variant,intron_variant							1		-1	KLK4	HGNC	6365	protein_coding	YES	CCDS12809.1	ENSP00000326159	Q9Y5K2	Q96RU5,Q96PT1,Q96JD9	UPI0000037168	NM_004917.3				2/4																		LOW	1	SNV													1	.	TGC	.	.																					51412500
MIR521-2	574481	.	GRCh37	19	54216794	54216794	+	5'Flank	SNP	G	G	T	rs7508562		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																			ENST00000384818		74	57	17	113			MIR521-2,upstream_gene_variant,,ENST00000384818,;MIR518C,downstream_gene_variant,,ENST00000384822,;MIR517A,downstream_gene_variant,,ENST00000385001,;MIR524,downstream_gene_variant,,ENST00000385242,;MIR519D,downstream_gene_variant,,ENST00000385246,;	T	ENSG00000207549	ENST00000384818	Transcript	upstream_gene_variant						rs7508562	1	3054	1	MIR521-2	HGNC	32113	miRNA	YES																												MODIFIER	1	SNV														.	GGT	.	.																					54216794
DNAAF3	352909	.	GRCh37	19	55672470	55672470	+	Missense_Mutation	SNP	T	T	C	rs2365725		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.1079A>G	p.Glu360Gly	p.E360G	ENST00000527223	8/12	11	3	8	4			DNAAF3,missense_variant,p.Glu360Gly,ENST00000527223,NM_001256714.1;DNAAF3,missense_variant,p.Glu339Gly,ENST00000391720,NM_178837.4,NM_001256715.1,NM_001256716.1;DNAAF3,missense_variant,p.Glu292Gly,ENST00000524407,;DNAAF3,missense_variant,p.Glu238Gly,ENST00000455045,;TNNI3,upstream_gene_variant,,ENST00000344887,NM_000363.4;DNAAF3,downstream_gene_variant,,ENST00000526003,;DNAAF3,downstream_gene_variant,,ENST00000532817,;DNAAF3,downstream_gene_variant,,ENST00000534170,;TNNI3,upstream_gene_variant,,ENST00000586858,;DNAAF3,upstream_gene_variant,,ENST00000588076,;TNNI3,upstream_gene_variant,,ENST00000588882,;CTD-2587H24.5,non_coding_transcript_exon_variant,,ENST00000591665,;DNAAF3,non_coding_transcript_exon_variant,,ENST00000527292,;DNAAF3,downstream_gene_variant,,ENST00000527166,;DNAAF3,downstream_gene_variant,,ENST00000528476,;TNNI3,upstream_gene_variant,,ENST00000586669,;DNAAF3,upstream_gene_variant,,ENST00000587789,;TNNI3,upstream_gene_variant,,ENST00000590463,;DNAAF3,3_prime_UTR_variant,,ENST00000528412,;DNAAF3,non_coding_transcript_exon_variant,,ENST00000533527,;DNAAF3,downstream_gene_variant,,ENST00000526959,;DNAAF3,downstream_gene_variant,,ENST00000534214,;TNNI3,upstream_gene_variant,,ENST00000585806,;TNNI3,upstream_gene_variant,,ENST00000586446,;DNAAF3,downstream_gene_variant,,ENST00000586877,;TNNI3,upstream_gene_variant,,ENST00000587176,;CTD-2587H24.4,upstream_gene_variant,,ENST00000587871,;	C	ENSG00000167646	ENST00000527223	Transcript	missense_variant	1081/2228	1079/1827	360/608	E/G	gAg/gGg	rs2365725	1		-1	DNAAF3	HGNC	30492	protein_coding	YES	CCDS58680.1	ENSP00000436975	Q8N9W5	H0YD30,H0YCU4	UPI000013E6F1	NM_001256714.1	deleterious(0.01)	benign(0.234)	8/12		Pfam:PF14740,PANTHER:PTHR22118,PANTHER:PTHR22118:SF4	0.2276	0.5234	0.1455		0.0913	0.1421	0.1145	0.3667	0.1225	likely_benign,benign		25741868,24033266					MODERATE	1	SNV			1										1	.	CTC	.	.												0.1591	0.4908	0.1169	0.2512	0.07956	0.0948	0.1557	0.1975	0.1373	55672470
ZNF773	374928	.	GRCh37	19	58011447	58011447	+	5'UTR	SNP	C	C	T	rs138317120		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.-2C>T			ENST00000282292	1/4	32	21	11	7			ZNF773,5_prime_UTR_variant,,ENST00000599847,;ZNF773,5_prime_UTR_variant,,ENST00000282292,NM_198542.1;ZNF773,5_prime_UTR_variant,,ENST00000598770,;ZNF773,5_prime_UTR_variant,,ENST00000593916,;ZNF773,5_prime_UTR_variant,,ENST00000597061,;AC003005.4,intron_variant,,ENST00000599674,;AC003005.4,intron_variant,,ENST00000601674,;ZNF773,upstream_gene_variant,,ENST00000601958,;,regulatory_region_variant,,ENSR00000111805,;	T	ENSG00000152439	ENST00000282292	Transcript	5_prime_UTR_variant	139/2206					rs138317120	1		1	ZNF773	HGNC	30487	protein_coding	YES	CCDS33134.1	ENSP00000282292	Q6PK81		UPI00001BD93D	NM_198542.1			1/4			0.0855	0.0076	0.0331		0.1766	0.0606	0.1595	0.01384	0.06272								MODIFIER	1	SNV														.	CCG	.	.												0.07601	0.01262	0.02621	0.06367	0.1983	0.06724	0.06574	0.0625	0.1388	58011447
ZNF544	27300	.	GRCh37	19	58773290	58773290	+	Missense_Mutation	SNP	G	G	C			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.1318G>C	p.Glu440Gln	p.E440Q	ENST00000269829	7/7	163	125	38	106	106	0	ZNF544,missense_variant,p.Glu440Gln,ENST00000269829,NM_014480.2;ZNF544,missense_variant,p.Glu412Gln,ENST00000600220,;ZNF544,missense_variant,p.Glu440Gln,ENST00000596652,;ZNF544,missense_variant,p.Glu412Gln,ENST00000600044,;ZNF544,missense_variant,p.Glu412Gln,ENST00000415203,;ZNF544,missense_variant,p.Glu298Gln,ENST00000599953,;ZNF544,3_prime_UTR_variant,,ENST00000599227,;ZNF544,3_prime_UTR_variant,,ENST00000596825,;ZNF544,intron_variant,,ENST00000595981,;ZNF544,intron_variant,,ENST00000596929,;ZNF544,downstream_gene_variant,,ENST00000594384,;CTD-3138B18.5,intron_variant,,ENST00000597230,;CTD-3138B18.6,upstream_gene_variant,,ENST00000595301,;ZNF544,downstream_gene_variant,,ENST00000598880,;ZNF544,3_prime_UTR_variant,,ENST00000596677,;CTD-3138B18.4,intron_variant,,ENST00000600029,;,regulatory_region_variant,,ENSR00001614167,;	C	ENSG00000198131	ENST00000269829	Transcript	missense_variant	1792/3512	1318/2148	440/715	E/Q	Gaa/Caa	COSV54138353	1		1	ZNF544	HGNC	16759	protein_coding	YES	CCDS12973.1	ENSP00000269829	Q6NX49	O14844,M0QY11	UPI000013D856	NM_014480.2	tolerated(0.12)	benign(0.091)	7/7		Gene3D:3.30.160.60,Pfam:PF13465,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,PANTHER:PTHR24377,SMART:SM00355,Superfamily:SSF57667											1						MODERATE	1	SNV			1											.	TGA	.	.																					58773290
C20orf96	140680	.	GRCh37	20	260005	260005	+	Intron	SNP	T	T	C	rs369425055		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.307-34A>G			ENST00000360321		19	8	11	6			C20orf96,intron_variant,,ENST00000360321,NM_153269.2,NM_080571.1;C20orf96,intron_variant,,ENST00000382369,;C20orf96,intron_variant,,ENST00000400269,;,regulatory_region_variant,,ENSR00001214111,;	C	ENSG00000196476	ENST00000360321	Transcript	intron_variant						rs369425055	1		-1	C20orf96	HGNC	16227	protein_coding	YES	CCDS12994.1	ENSP00000353470	Q9NUD7		UPI00001285F1	NM_153269.2,NM_080571.1				4/10		0.0010		0.0029			0.003											MODIFIER	1	SNV														.	CTG	.	.												0.003589	0.0003029	0.004027	0.04284			0.001924	0.006346	0.0008193	260005
CSTL1	128817	.	GRCh37	20	23420938	23420938	+	Silent	SNP	C	C	T			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.34C>T	p.Leu12=	p.L12=	ENST00000347397	2/4	181	160	21	88	88	0	CSTL1,synonymous_variant,p.Leu12=,ENST00000347397,NM_138283.1;CSTL1,synonymous_variant,p.Leu12=,ENST00000246020,;CSTL1,non_coding_transcript_exon_variant,,ENST00000472140,;CSTL1,upstream_gene_variant,,ENST00000485969,;	T	ENSG00000125823	ENST00000347397	Transcript	synonymous_variant	280/736	34/438	12/145	L	Ctg/Ttg	COSV55679089	1		1	CSTL1	HGNC	15958	protein_coding	YES	CCDS13153.1	ENSP00000344907	Q9H114		UPI000003E836	NM_138283.1			2/4		PANTHER:PTHR11413,PANTHER:PTHR11413:SF9,Cleavage_site_(Signalp):SignalP-noTM,Low_complexity_(Seg):seg											1						LOW	1	SNV			1											.	GCT	.	.																					23420938
FAM182B	548321	.	GRCh37	20	25755889	25755889	+	Missense_Mutation	SNP	A	A	T			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.67T>A	p.Cys23Ser	p.C23S	ENST00000376403	3/3	123	70	53	46	42	0	FAM182B,missense_variant,p.Cys23Ser,ENST00000376403,;FAM182B,missense_variant,p.Cys20Ser,ENST00000376404,;FAM182B,missense_variant,p.Cys31Ser,ENST00000584071,;FAM182B,non_coding_transcript_exon_variant,,ENST00000478164,;FAM182B,non_coding_transcript_exon_variant,,ENST00000582267,;FAM182B,non_coding_transcript_exon_variant,,ENST00000485279,;FAM182B,non_coding_transcript_exon_variant,,ENST00000453481,;FAM182B,downstream_gene_variant,,ENST00000584356,;	T	ENSG00000175170	ENST00000376403	Transcript	missense_variant	446/1681	67/459	23/152	C/S	Tgc/Agc	COSV64520055	1		-1	FAM182B	HGNC	34503	protein_coding	YES		ENSP00000365585	Q5T319		UPI000047001E		tolerated_low_confidence(0.1)	benign(0.3)	3/3													1						MODERATE	1	SNV			1											.	CAG	.	.																					25755889
FAM182A	728882	.	GRCh37	20	26061750	26061750	+	Intron	SNP	T	T	A	rs113003523		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																n.820-50T>A			ENST00000376398		50	45	5	32	32	0	FAM182A,intron_variant,,ENST00000376398,;FAM182A,downstream_gene_variant,,ENST00000471057,;FAM182A,intron_variant,,ENST00000415411,;FAM182A,intron_variant,,ENST00000482133,;	A	ENSG00000125804	ENST00000376398	Transcript	intron_variant,non_coding_transcript_variant						rs113003523	1		1	FAM182A	HGNC	16222	lincRNA	YES										3/4																		MODIFIER	1	SNV														.	TTT	.	.												0.001331	0.0005153	0.0001569	0.0002773	0.0001441	0.002449	0.001961	0.0004177	0.001701	26061750
GDF5	8200	.	GRCh37	20	34022387	34022387	+	Missense_Mutation	SNP	A	A	C	rs224331		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.826T>G	p.Ser276Ala	p.S276A	ENST00000374372	4/4	40	16	24	5			GDF5,missense_variant,p.Ser276Ala,ENST00000374372,;GDF5,missense_variant,p.Ser276Ala,ENST00000374369,NM_000557.2;GDF5OS,missense_variant,p.Glu144Ala,ENST00000374375,;	C	ENSG00000125965	ENST00000374372	Transcript	missense_variant	1330/2572	826/1506	276/501	S/A	Tcc/Gcc	rs224331	1		-1	GDF5	HGNC	4220	protein_coding	YES	CCDS13254.1	ENSP00000363492	P43026	D3YR76,D3YQT0	UPI000002E33B		tolerated(0.77)	benign(0)	4/4		PANTHER:PTHR11848:SF44,PANTHER:PTHR11848,Pfam:PF00688	0.3840	0.466	0.2608		0.2857	0.3539	0.4928	0.4147	0.346	benign		25741868,31145760					MODERATE	1	SNV			1										1	.	GAG	.	.												0.3524	0.4523	0.2238	0.4044	0.2778	0.3899	0.3545	0.365	0.4455	34022387
MICAL3	57553	.	GRCh37	22	18300594	18300594	+	Silent	SNP	G	A	A	rs11704160		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	A																c.4833C>T	p.Asp1611=	p.D1611=	ENST00000441493	26/32	16	0	16	7			MICAL3,synonymous_variant,p.Asp1611=,ENST00000441493,NM_015241.2;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000580469,;	A	ENSG00000243156	ENST00000441493	Transcript	synonymous_variant	5186/9445	4833/6009	1611/2002	D	gaC/gaT	rs11704160	1		-1	MICAL3	HGNC	24694	protein_coding	YES	CCDS46659.1	ENSP00000416015	Q7RTP6	C9J922,A8K0E1	UPI0001823FDE	NM_015241.2			26/32		PANTHER:PTHR11915,PANTHER:PTHR11915:SF218	0.1512	0.028	0.1859		0.0863	0.3171	0.1892	0.07115	0.3287								LOW	1	SNV														.	CGT	.	.												0.2536	0.06549	0.1547	0.3944	0.08427	0.3026	0.3289	0.2865	0.2109	18300594
IGLV3-16	0	.	GRCh37	22	23089759	23089759	+	5'Flank	SNP	A	T	T	rs2040563		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																			ENST00000390311		4	0	4	1			IGLV3-16,upstream_gene_variant,,ENST00000390311,;,regulatory_region_variant,,ENSR00001237992,;,regulatory_region_variant,,ENSR00001649907,;,TF_binding_site_variant,,ENSM00523334187,;	T	ENSG00000211665	ENST00000390311	Transcript	upstream_gene_variant						rs2040563	1	111	1	IGLV3-16	HGNC	5901	IG_V_gene	YES		ENSP00000374846			UPI0000EE5A3C								0.8896	0.7695		0.9147	0.6362	0.7311										MODIFIER	1	SNV														.	GAG	.	.																					23089759
AKAP17A	8227	.	GRCh37	X	1712722	1712722	+	Missense_Mutation	SNP	A	A	C	rs748366947		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.367A>C	p.Thr123Pro	p.T123P	ENST00000313871	2/5	44	34	10	20	0	0	AKAP17A,missense_variant,p.Thr123Pro,ENST00000313871,NM_005088.2;AKAP17A,missense_variant,p.Thr123Pro,ENST00000381261,;AKAP17A,missense_variant,p.Thr123Pro,ENST00000474361,;	C	ENSG00000197976	ENST00000313871	Transcript	missense_variant	563/3204	367/2088	123/695	T/P	Acc/Ccc	rs748366947,COSV58308304	1		1	AKAP17A	HGNC	18783	protein_coding	YES	CCDS14116.1	ENSP00000324827	Q02040		UPI00001AF072	NM_005088.2	deleterious(0.01)	probably_damaging(0.943)	2/5		PANTHER:PTHR12484,PANTHER:PTHR12484:SF2											0,1						MODERATE	1	SNV			0,1											.	CAC	.	.												0.007297	0.002368	0.0008048	0.005993	0.001053	0.03322	0.006807	0.005242	0.007529	1712722
NLGN4X	57502	.	GRCh37	X	5810784	5810784	+	3'UTR	SNP	C	C	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.*74G>A			ENST00000381095	6/6	104	53	21	124			NLGN4X,3_prime_UTR_variant,,ENST00000381095,NM_181332.1,NM_001282146.1,NM_001282145.1;NLGN4X,3_prime_UTR_variant,,ENST00000381093,;NLGN4X,3_prime_UTR_variant,,ENST00000275857,NM_020742.2;NLGN4X,3_prime_UTR_variant,,ENST00000381092,;NLGN4X,3_prime_UTR_variant,,ENST00000538097,;NLGN4X,intron_variant,,ENST00000477079,;	T	ENSG00000146938	ENST00000381095	Transcript	3_prime_UTR_variant	3153/5870						1		-1	NLGN4X	HGNC	14287	protein_coding	YES	CCDS14126.1	ENSP00000370485	Q8N0W4	B3KMT6	UPI0000072EC5	NM_181332.1,NM_001282146.1,NM_001282145.1			6/6																			MODIFIER	1	SNV													1	.	CCT	.	.																					5810784
CXorf58	254158	.	GRCh37	X	23956735	23956735	+	Missense_Mutation	SNP	G	G	A			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	G	G																c.857G>A	p.Arg286His	p.R286H	ENST00000379211	8/9	119	95	24	153	152	0	CXorf58,missense_variant,p.Arg286His,ENST00000379211,NM_001169574.1,NM_152761.2;	A	ENSG00000165182	ENST00000379211	Transcript	missense_variant	1406/1752	857/999	286/332	R/H	cGt/cAt	COSV64858744	1		1	CXorf58	HGNC	26356	protein_coding	YES	CCDS14209.1	ENSP00000368511	Q96LI9		UPI00001AEC5F	NM_001169574.1,NM_152761.2	deleterious(0.03)	probably_damaging(0.955)	8/9													1						MODERATE	1	SNV			1											.	CGT	.	.																					23956735
CASK	8573	.	GRCh37	X	41379771	41379771	+	Missense_Mutation	SNP	T	T	C			TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.2668A>G	p.Ile890Val	p.I890V	ENST00000378166	27/27	187	127	60	166	163	0	CASK,missense_variant,p.Ile890Val,ENST00000318588,;CASK,missense_variant,p.Ile878Val,ENST00000361962,;CASK,missense_variant,p.Ile866Val,ENST00000421587,NM_001126055.2;CASK,missense_variant,p.Ile895Val,ENST00000378163,;CASK,missense_variant,p.Ile878Val,ENST00000378158,;CASK,missense_variant,p.Ile890Val,ENST00000378166,NM_003688.3;CASK,missense_variant,p.Ile487Val,ENST00000378179,;CASK,missense_variant,p.Ile867Val,ENST00000442742,NM_001126054.2;CASK,missense_variant,p.Ile350Val,ENST00000378168,;CASK-AS1,intron_variant,,ENST00000451126,;	C	ENSG00000147044	ENST00000378166	Transcript	missense_variant	2695/3123	2668/2766	890/921	I/V	Atc/Gtc	COSV59374926	1		-1	CASK	HGNC	1497	protein_coding	YES	CCDS14257.1	ENSP00000367408	O14936		UPI000013DA91	NM_003688.3	tolerated(1)	benign(0)	27/27		Gene3D:3.40.50.300,Pfam:PF00625,PROSITE_profiles:PS50052,PANTHER:PTHR23122,PANTHER:PTHR23122:SF40,SMART:SM00072,Superfamily:SSF52540											1						MODERATE	1	SNV			1										1	.	ATA	.	.																					41379771
PRRG3	79057	.	GRCh37	X	150868861	150868861	+	Intron	SNP	C	C	T	rs41302168		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.169-117C>T			ENST00000370353		5	1	4	6			PRRG3,intron_variant,,ENST00000370353,;PRRG3,intron_variant,,ENST00000370354,;PRRG3,intron_variant,,ENST00000538575,NM_024082.3;PRRG3,upstream_gene_variant,,ENST00000448324,;PRRG3,downstream_gene_variant,,ENST00000448726,;	T	ENSG00000130032	ENST00000370353	Transcript	intron_variant						rs41302168,COSV64851455	1		1	PRRG3	HGNC	30798	protein_coding	YES	CCDS14699.1	ENSP00000359378	Q9BZD7	C9J7E6	UPI00004578A5					3/3		0.0710	0.1755	0.0477		0.0183	0.0522	0.0181				0,1						MODIFIER	1	SNV			0,1											.	TCT	.	.																					150868861
L1CAM	3897	.	GRCh37	X	153132281	153132281	+	Missense_Mutation	SNP	C	C	T	rs137852525		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.2254G>A	p.Val752Met	p.V752M	ENST00000370060	19/29	54	41	13	61	61	0	L1CAM,missense_variant,p.Val752Met,ENST00000370060,NM_001278116.1;L1CAM,missense_variant,p.Val754Met,ENST00000543994,;L1CAM,missense_variant,p.Val752Met,ENST00000370057,NM_024003.3,NM_000425.4;L1CAM,missense_variant,p.Val754Met,ENST00000538883,;L1CAM,missense_variant,p.Val747Met,ENST00000361981,NM_001143963.2;L1CAM,missense_variant,p.Val747Met,ENST00000370055,;L1CAM,missense_variant,p.Val752Met,ENST00000361699,;L1CAM,missense_variant,p.Val173Met,ENST00000455590,;L1CAM,upstream_gene_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000439496,;L1CAM,upstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000484652,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,downstream_gene_variant,,ENST00000496122,;	T	ENSG00000198910	ENST00000370060	Transcript	missense_variant	2444/5113	2254/3774	752/1257	V/M	Gtg/Atg	rs137852525,CM970859,COSV62830040	1		-1	L1CAM	HGNC	6470	protein_coding	YES	CCDS14733.1	ENSP00000359077	P32004	Q86SE4,Q7Z3Z9,Q7Z2J9,Q7Z2J8,Q7Z2J6,Q7Z2J0,Q7Z2I3,Q7Z2H2,Q7Z2F9,E9PHJ4,E7EPI4	UPI0000126E89	NM_001278116.1	deleterious(0)	probably_damaging(1)	19/29		Gene3D:2.60.40.10,Pfam:PF00041,PROSITE_profiles:PS50853,PANTHER:PTHR10489,PANTHER:PTHR10489:SF42,SMART:SM00060,Superfamily:SSF49265										pathogenic	0,0,1	11857550					MODERATE	1	SNV			1,1,1										1	.	ACG	.	.												5.489e-06						1.235e-05			153132281
FLNA	2316	.	GRCh37	X	153595171	153595171	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	C	C																c.916G>A	p.Val306Met	p.V306M	ENST00000369850	6/48	202	194	8	129	127	0	FLNA,missense_variant,p.Val306Met,ENST00000422373,NM_001456.3;FLNA,missense_variant,p.Val306Met,ENST00000369850,NM_001110556.1;FLNA,missense_variant,p.Val306Met,ENST00000360319,;FLNA,missense_variant,p.Val306Met,ENST00000344736,;FLNA,missense_variant,p.Val292Met,ENST00000420627,;FLNA,upstream_gene_variant,,ENST00000465144,;	T	ENSG00000196924	ENST00000369850	Transcript	missense_variant	1153/8382	916/7944	306/2647	V/M	Gtg/Atg		1		-1	FLNA	HGNC	3754	protein_coding	YES	CCDS48194.1	ENSP00000358866	P21333	Q96C61,Q86TQ3,Q6NXF2,Q60FE5	UPI000013C596	NM_001110556.1	deleterious(0)	probably_damaging(0.973)	6/48		Gene3D:2.60.40.10,Pfam:PF00630,PROSITE_profiles:PS50194,PANTHER:PTHR11915,PANTHER:PTHR11915:SF173,SMART:SM00557,Superfamily:SSF81296																	MODERATE	1	SNV													1	.	ACA	.	.																					153595171