TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.indel.capture.tcga.txt 19.3 KB
Newer Older
Pradat Yoann's avatar
Pradat Yoann committed
1 2 3 4 5 6 7 8 9 10
n_GT	n_SS	n_TIR	n_TAR	n_DP	n_DP4	n_AD	n_depth	n_ref_count	n_alt_count	t_GT	t_SS	t_TIR	t_TAR	t_DP	t_DP4	t_AD	t_depth	t_ref_count	t_alt_count	Variant_Quality	Filter_VCF	Hugo_Symbol_VCF2MAF	Entrez_Gene_Id_VCF2MAF	Center_VCF2MAF	NCBI_Build_VCF2MAF	Chromosome_VCF2MAF	Start_Position_VCF2MAF	End_Position_VCF2MAF	Strand_VCF2MAF	Variant_Classification_VCF2MAF	Variant_Type_VCF2MAF	Reference_Allele_VCF2MAF	Tumor_Seq_Allele1_VCF2MAF	Tumor_Seq_Allele2_VCF2MAF	dbSNP_RS_VCF2MAF	dbSNP_Val_Status_VCF2MAF	Tumor_Sample_Barcode_VCF2MAF	Matched_Norm_Sample_Barcode_VCF2MAF	Match_Norm_Seq_Allele1_VCF2MAF	Match_Norm_Seq_Allele2_VCF2MAF	Tumor_Validation_Allele1_VCF2MAF	Tumor_Validation_Allele2_VCF2MAF	Match_Norm_Validation_Allele1_VCF2MAF	Match_Norm_Validation_Allele2_VCF2MAF	Verification_Status_VCF2MAF	Validation_Status_VCF2MAF	Mutation_Status_VCF2MAF	Sequencing_Phase_VCF2MAF	Sequence_Source_VCF2MAF	Validation_Method_VCF2MAF	Score_VCF2MAF	BAM_File_VCF2MAF	Sequencer_VCF2MAF	Tumor_Sample_UUID_VCF2MAF	Matched_Norm_Sample_UUID_VCF2MAF	HGVSc_VCF2MAF	HGVSp_VCF2MAF	HGVSp_Short_VCF2MAF	Transcript_ID_VCF2MAF	Exon_Number_VCF2MAF	t_depth_VCF2MAF	t_ref_count_VCF2MAF	t_alt_count_VCF2MAF	n_depth_VCF2MAF	n_ref_count_VCF2MAF	n_alt_count_VCF2MAF	all_effects_VCF2MAF	Allele_VCF2MAF	Gene_VCF2MAF	Feature_VCF2MAF	Feature_type_VCF2MAF	Consequence_VCF2MAF	cDNA_position_VCF2MAF	CDS_position_VCF2MAF	Protein_position_VCF2MAF	Amino_acids_VCF2MAF	Codons_VCF2MAF	Existing_variation_VCF2MAF	ALLELE_NUM_VCF2MAF	DISTANCE_VCF2MAF	STRAND_VEP_VCF2MAF	SYMBOL_VCF2MAF	SYMBOL_SOURCE_VCF2MAF	HGNC_ID_VCF2MAF	BIOTYPE_VCF2MAF	CANONICAL_VCF2MAF	CCDS_VCF2MAF	ENSP_VCF2MAF	SWISSPROT_VCF2MAF	TREMBL_VCF2MAF	UNIPARC_VCF2MAF	RefSeq_VCF2MAF	SIFT_VCF2MAF	PolyPhen_VCF2MAF	EXON_VCF2MAF	INTRON_VCF2MAF	DOMAINS_VCF2MAF	AF_VCF2MAF	AFR_AF_VCF2MAF	AMR_AF_VCF2MAF	ASN_AF_VCF2MAF	EAS_AF_VCF2MAF	EUR_AF_VCF2MAF	SAS_AF_VCF2MAF	AA_AF_VCF2MAF	EA_AF_VCF2MAF	CLIN_SIG_VCF2MAF	SOMATIC_VCF2MAF	PUBMED_VCF2MAF	MOTIF_NAME_VCF2MAF	MOTIF_POS_VCF2MAF	HIGH_INF_POS_VCF2MAF	MOTIF_SCORE_CHANGE_VCF2MAF	IMPACT_VCF2MAF	PICK_VCF2MAF	VARIANT_CLASS_VCF2MAF	TSL_VCF2MAF	HGVS_OFFSET_VCF2MAF	PHENO_VCF2MAF	MINIMISED_VCF2MAF	ExAC_AF_VCF2MAF	ExAC_AF_AFR_VCF2MAF	ExAC_AF_AMR_VCF2MAF	ExAC_AF_EAS_VCF2MAF	ExAC_AF_FIN_VCF2MAF	ExAC_AF_NFE_VCF2MAF	ExAC_AF_OTH_VCF2MAF	ExAC_AF_SAS_VCF2MAF	GENE_PHENO_VCF2MAF	FILTER_VCF2MAF	flanking_bps_VCF2MAF	vcf_id_VCF2MAF	vcf_qual_VCF2MAF	ExAC_AF_Adj_VCF2MAF	ExAC_AC_AN_Adj_VCF2MAF	ExAC_AC_AN_VCF2MAF	ExAC_AC_AN_AFR_VCF2MAF	ExAC_AC_AN_AMR_VCF2MAF	ExAC_AC_AN_EAS_VCF2MAF	ExAC_AC_AN_FIN_VCF2MAF	ExAC_AC_AN_NFE_VCF2MAF	ExAC_AC_AN_OTH_VCF2MAF	ExAC_AC_AN_SAS_VCF2MAF	ExAC_FILTER_VCF2MAF	gnomAD_AF_VCF2MAF	gnomAD_AFR_AF_VCF2MAF	gnomAD_AMR_AF_VCF2MAF	gnomAD_ASJ_AF_VCF2MAF	gnomAD_EAS_AF_VCF2MAF	gnomAD_FIN_AF_VCF2MAF	gnomAD_NFE_AF_VCF2MAF	gnomAD_OTH_AF_VCF2MAF	gnomAD_SAS_AF_VCF2MAF	vcf_pos_VCF2MAF	#Uploaded_variation_VEP	Location_VEP	Allele_VEP	Gene_VEP	Feature_VEP	Feature_type_VEP	Consequence_VEP	cDNA_position_VEP	CDS_position_VEP	Protein_position_VEP	Amino_acids_VEP	Codons_VEP	Existing_variation_VEP	Extra_VEP	IMPACT_VEP	STRAND_VEP	SYMBOL_VEP	SYMBOL_SOURCE_VEP	HGNC_ID_VEP	BIOTYPE_VEP	CANONICAL_VEP	CCDS_VEP	ENSP_VEP	SWISSPROT_VEP	UNIPARC_VEP	INTRON_VEP	HGVSc_VEP	AFR_AF_VEP	AMR_AF_VEP	EAS_AF_VEP	EUR_AF_VEP	SAS_AF_VEP	MAX_AF_VEP	MAX_AF_POPS_VEP	TREMBL_VEP	EXON_VEP	HGVSp_VEP	gnomAD_AF_VEP	gnomAD_AFR_AF_VEP	gnomAD_AMR_AF_VEP	gnomAD_ASJ_AF_VEP	gnomAD_EAS_AF_VEP	gnomAD_FIN_AF_VEP	gnomAD_NFE_AF_VEP	gnomAD_OTH_AF_VEP	gnomAD_SAS_AF_VEP	HGVS_OFFSET_VEP	Tumor_Sample	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Tumor_Sample_Site
0/0	2			11		11,0	11.0	11.0	0.0	0/1	2			6		4,2	6.0			50	PASS	FAM131C	348487	.	GRCh37	1	16386305	16386306	+	Intron	INS	-	-	C	rs372070031		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	-	-																c.451+58dup			ENST00000375662								FAM131C,intron_variant,,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,intron_variant,,ENST00000494078,;	C	ENSG00000185519	ENST00000375662	Transcript	intron_variant						rs372070031	1		-1	FAM131C	HGNC	26717	protein_coding	YES	CCDS41270.1	ENSP00000364814	Q96AQ9		UPI000022B016	NM_182623.2				5/6			0.2731	0.3573		0.3581	0.3757	0.5051										MODIFIER	1	insertion														PASS	GGC	rs143272992	50																					16386305	rs143272992	1:16386305-16386306	C	ENSG00000185519	ENST00000375662.4	Transcript	intron_variant	-	-	-	-	-	rs372070031	IMPACT=MODIFIER;STRAND=-1;SYMBOL=FAM131C;SYMBOL_SOURCE=HGNC;HGNC_ID=26717;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS41270.1;ENSP=ENSP00000364814;SWISSPROT=Q96AQ9;UNIPARC=UPI000022B016;INTRON=5/6;HGVSc=ENST00000375662.4:c.451+58dup;AFR_AF=0.2731;AMR_AF=0.3573;EAS_AF=0.3581;EUR_AF=0.3757;SAS_AF=0.5051;MAX_AF=0.5051;MAX_AF_POPS=SAS	MODIFIER	-1	FAM131C	HGNC	26717	protein_coding	YES	CCDS41270.1	ENSP00000364814	Q96AQ9	UPI000022B016	5/6	ENST00000375662.4:c.451+58dup	0.2731	0.3573	0.3581	0.3757	0.5051	0.5051	SAS														TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			6		6,0	6.0	6.0	0.0	0/1	2			6		4,2	6.0			50	PASS	ZIC4	84107	.	GRCh37	3	147121630	147121631	+	Intron	DEL	TC	TC	-	rs142316820		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	TC	TC																c.135+120_135+121del			ENST00000525172								ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,;	-	ENSG00000174963	ENST00000525172	Transcript	intron_variant						rs142316820	1		-1	ZIC4	HGNC	20393	protein_coding	YES	CCDS54652.1	ENSP00000435509	Q8N9L1	C9JZU7,C9JD04,C9J6T3,B3KPI4	UPI0001914D88	NM_001168378.1				1/4																		MODIFIER	1	deletion													1.0	PASS	GATCT	.	50																					147121629	3_147121630_TC/-	3:147121630-147121631	-	ENSG00000174963	ENST00000525172.2	Transcript	intron_variant	-	-	-	-	-	rs142316820	IMPACT=MODIFIER;STRAND=-1;SYMBOL=ZIC4;SYMBOL_SOURCE=HGNC;HGNC_ID=20393;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS54652.1;ENSP=ENSP00000435509;SWISSPROT=Q8N9L1;TREMBL=C9JZU7,C9JD04,C9J6T3,B3KPI4;UNIPARC=UPI0001914D88;INTRON=1/4;HGVSc=ENST00000525172.2:c.135+120_135+121del	MODIFIER	-1	ZIC4	HGNC	20393	protein_coding	YES	CCDS54652.1	ENSP00000435509	Q8N9L1	UPI0001914D88	1/4	ENST00000525172.2:c.135+120_135+121del								C9JZU7,C9JD04,C9J6T3,B3KPI4													TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			7		7,0	7.0	7.0	0.0	0/1	2			6		2,4	6.0			50	PASS	EIF4G1	1981	.	GRCh37	3	184043926	184043927	+	Intron	DEL	AC	AC	-	rs34901174		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	AC	AC																c.3243+217_3243+218del			ENST00000424196								EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,;	-	ENSG00000114867	ENST00000424196	Transcript	intron_variant						rs34901174	1		1	EIF4G1	HGNC	3296	protein_coding	YES	CCDS54687.1	ENSP00000416255	Q04637	Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556	UPI00015E0966					20/31																		MODIFIER	1	deletion													1.0	PASS	AAACA	rs112208190	50																					184043925	rs112208190	3:184043926-184043927	-	ENSG00000114867	ENST00000424196.1	Transcript	intron_variant	-	-	-	-	-	rs34901174	IMPACT=MODIFIER;STRAND=1;SYMBOL=EIF4G1;SYMBOL_SOURCE=HGNC;HGNC_ID=3296;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS54687.1;ENSP=ENSP00000416255;SWISSPROT=Q04637;TREMBL=Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556;UNIPARC=UPI00015E0966;INTRON=20/31;HGVSc=ENST00000424196.1:c.3243+217_3243+218del	MODIFIER	1	EIF4G1	HGNC	3296	protein_coding	YES	CCDS54687.1	ENSP00000416255	Q04637	UPI00015E0966	20/31	ENST00000424196.1:c.3243+217_3243+218del								Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556													TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			22		22,0	22.0	22.0	0.0	0/1	2			6		4,2	6.0			50	PASS	STEAP1B	256227	.	GRCh37	7	22533452	22533453	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	CA	CA																c.87_88del	p.His29GlnfsTer24	p.H29Qfs*24	ENST00000404369	3/5							STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,;	-	ENSG00000105889	ENST00000404369	Transcript	frameshift_variant,splice_region_variant	503-504/1515	87-88/1029	29-30/342	HE/QX	caTGag/caag		1		-1	STEAP1B	HGNC	41907	protein_coding	YES	CCDS56469.1	ENSP00000384370		C9JL51,C9JE84,B5MCI2	UPI000173A267	NM_001164460.1			3/5		PANTHER:PTHR14239:SF3,PANTHER:PTHR14239																	HIGH	1	deletion														PASS	CTCAT	rs116873396	50																					22533451	rs116873396	7:22533452-22533453	-	ENSG00000105889	ENST00000404369.4	Transcript	frameshift_variant,splice_region_variant	503-504	87-88	29-30	HE/QX	caTGag/caag	-	IMPACT=HIGH;STRAND=-1;SYMBOL=STEAP1B;SYMBOL_SOURCE=HGNC;HGNC_ID=41907;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS56469.1;ENSP=ENSP00000384370;TREMBL=C9JL51,C9JE84,B5MCI2;UNIPARC=UPI000173A267;EXON=3/5;HGVSc=ENST00000404369.4:c.87_88del;HGVSp=ENSP00000384370.4:p.His29GlnfsTer24	HIGH	-1	STEAP1B	HGNC	41907	protein_coding	YES	CCDS56469.1	ENSP00000384370		UPI000173A267		ENST00000404369.4:c.87_88del								C9JL51,C9JE84,B5MCI2	3/5	ENSP00000384370.4:p.His29GlnfsTer24											TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			31		31,0	31.0	31.0	0.0	0/1	2			6		4,2	6.0			50	PASS	TEX12	56158	.	GRCh37	11	112042480	112042480	+	Intron	DEL	T	T	-	rs1225064086		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.228-9del			ENST00000280358								TEX12,intron_variant,,ENST00000280358,NM_031275.4;TEX12,intron_variant,,ENST00000530752,;AP002884.3,intron_variant,,ENST00000532612,;BCO2,upstream_gene_variant,,ENST00000357685,;BCO2,upstream_gene_variant,,ENST00000361053,NM_001256398.1;BCO2,upstream_gene_variant,,ENST00000393032,NM_031938.5;BCO2,upstream_gene_variant,,ENST00000438022,;BCO2,upstream_gene_variant,,ENST00000526088,NM_001037290.2,NM_001256397.1;BCO2,upstream_gene_variant,,ENST00000531169,;BCO2,upstream_gene_variant,,ENST00000532593,NM_001256400.1;RP11-356J5.4,intron_variant,,ENST00000527589,;SDHD,intron_variant,,ENST00000525468,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000531744,;SDHD,intron_variant,,ENST00000532699,;BCO2,upstream_gene_variant,,ENST00000460924,;BCO2,upstream_gene_variant,,ENST00000461480,;BCO2,upstream_gene_variant,,ENST00000494860,;BCO2,upstream_gene_variant,,ENST00000527939,;BCO2,upstream_gene_variant,,ENST00000531003,;BCO2,upstream_gene_variant,,ENST00000534122,;BCO2,upstream_gene_variant,,ENST00000534550,;	-	ENSG00000150783	ENST00000280358	Transcript	intron_variant						rs1225064086	1		1	TEX12	HGNC	11734	protein_coding	YES	CCDS31679.1	ENSP00000280358	Q9BXU0		UPI00001377E3	NM_031275.4				4/4																		MODIFIER	1	deletion														PASS	ACTT	.	50												1.711e-05	8.319e-05			8.285e-05		1.133e-05			112042479	11_112042480_T/-	11:112042480	-	ENSG00000150783	ENST00000280358.4	Transcript	intron_variant	-	-	-	-	-	rs1225064086	IMPACT=MODIFIER;STRAND=1;SYMBOL=TEX12;SYMBOL_SOURCE=HGNC;HGNC_ID=11734;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS31679.1;ENSP=ENSP00000280358;SWISSPROT=Q9BXU0;UNIPARC=UPI00001377E3;INTRON=4/4;HGVSc=ENST00000280358.4:c.228-9del;gnomAD_AF=1.711e-05;gnomAD_AFR_AF=8.319e-05;gnomAD_AMR_AF=0;gnomAD_ASJ_AF=0;gnomAD_EAS_AF=8.285e-05;gnomAD_FIN_AF=0;gnomAD_NFE_AF=1.133e-05;gnomAD_OTH_AF=0;gnomAD_SAS_AF=0;MAX_AF=8.319e-05;MAX_AF_POPS=gnomAD_AFR	MODIFIER	1	TEX12	HGNC	11734	protein_coding	YES	CCDS31679.1	ENSP00000280358	Q9BXU0	UPI00001377E3	4/4	ENST00000280358.4:c.228-9del						8.319e-05	gnomAD_AFR				1.711e-05	8.319e-05	0	0	8.285e-05	0	1.133e-05	0	0		TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			48		48,0	48.0	48.0	0.0	0/1	2			33		26,7	33.0			50	PASS	KMT2D	8085	.	GRCh37	12	49431403	49431404	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	-	-																c.9735dup	p.Pro3246ThrfsTer5	p.P3246Tfs*5	ENST00000301067	34/54							KMT2D,frameshift_variant,p.Pro3246ThrfsTer5,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,;	T	ENSG00000167548	ENST00000301067	Transcript	frameshift_variant	9735-9736/19419	9735-9736/16614	3245-3246/5537	-/X	-/A		1		-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	O14686	Q6PIA1,Q59FG6,F8VWW4	UPI0000EE84D6	NM_003482.3			34/54		PANTHER:PTHR22884,PANTHER:PTHR22884:SF324																	HIGH	1	insertion													1.0	PASS	GGT	.	50																					49431403	12_49431404_-/T	12:49431403-49431404	T	ENSG00000167548	ENST00000301067.7	Transcript	frameshift_variant	9735-9736	9735-9736	3245-3246	-/X	-/A	-	IMPACT=HIGH;STRAND=-1;SYMBOL=KMT2D;SYMBOL_SOURCE=HGNC;HGNC_ID=7133;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS44873.1;ENSP=ENSP00000301067;SWISSPROT=O14686;TREMBL=Q6PIA1,Q59FG6,F8VWW4;UNIPARC=UPI0000EE84D6;EXON=34/54;HGVSc=ENST00000301067.7:c.9735dup;HGVSp=ENSP00000301067.7:p.Pro3246ThrfsTer5	HIGH	-1	KMT2D	HGNC	7133	protein_coding	YES	CCDS44873.1	ENSP00000301067	O14686	UPI0000EE84D6		ENST00000301067.7:c.9735dup								Q6PIA1,Q59FG6,F8VWW4	34/54	ENSP00000301067.7:p.Pro3246ThrfsTer5											TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			47		47,0	47.0	47.0	0.0	0/1	2			6		4,2	6.0			50	PASS	PDS5B	23047	.	GRCh37	13	33332314	33332314	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	A	A																c.3148del	p.Thr1050GlnfsTer12	p.T1050Qfs*12	ENST00000315596	27/35							PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000315596,NM_015032.3;PDS5B,frameshift_variant,p.Thr4GlnfsTer12,ENST00000447833,;PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000450460,;	-	ENSG00000083642	ENST00000315596	Transcript	frameshift_variant	3332/7497	3146/4344	1049/1447	Q/X	cAa/ca		1		1	PDS5B	HGNC	20418	protein_coding	YES	CCDS41878.1	ENSP00000313851	Q9NTI5		UPI000006D4A9	NM_015032.3			27/35		PANTHER:PTHR12663,PANTHER:PTHR12663:SF1																	HIGH	1	deletion		2.0												PASS	ACAA	.	50																					33332313	13_33332314_A/-	13:33332314	-	ENSG00000083642	ENST00000315596.10	Transcript	frameshift_variant	3332	3146	1049	Q/X	cAa/ca	-	IMPACT=HIGH;STRAND=1;SYMBOL=PDS5B;SYMBOL_SOURCE=HGNC;HGNC_ID=20418;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS41878.1;ENSP=ENSP00000313851;SWISSPROT=Q9NTI5;UNIPARC=UPI000006D4A9;EXON=27/35;HGVSc=ENST00000315596.10:c.3148del;HGVSp=ENSP00000313851.10:p.Thr1050GlnfsTer12;HGVS_OFFSET=2	HIGH	1	PDS5B	HGNC	20418	protein_coding	YES	CCDS41878.1	ENSP00000313851	Q9NTI5	UPI000006D4A9		ENST00000315596.10:c.3148del									27/35	ENSP00000313851.10:p.Thr1050GlnfsTer12										2	TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			5		5,0	5.0	5.0	0.0	0/1	2			6		4,2	6.0			50	PASS	CCR7	1236	.	GRCh37	17	38712161	38712161	+	Intron	DEL	T	T	-	rs372297045		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	T	T																c.61-91del			ENST00000246657								CCR7,intron_variant,,ENST00000246657,NM_001838.3;CCR7,intron_variant,,ENST00000578085,;CCR7,intron_variant,,ENST00000579344,;	-	ENSG00000126353	ENST00000246657	Transcript	intron_variant						rs372297045	1		-1	CCR7	HGNC	1608	protein_coding	YES	CCDS11369.1	ENSP00000246657	P32248	J3KTN5,J3KSS9,A0N0Q0	UPI0000001C2F	NM_001838.3				2/2						0.004												MODIFIER	1	deletion													1.0	PASS	TCTT	.	50																					38712160	17_38712161_T/-	17:38712161	-	ENSG00000126353	ENST00000246657.2	Transcript	intron_variant	-	-	-	-	-	rs372297045	IMPACT=MODIFIER;STRAND=-1;SYMBOL=CCR7;SYMBOL_SOURCE=HGNC;HGNC_ID=1608;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS11369.1;ENSP=ENSP00000246657;SWISSPROT=P32248;TREMBL=J3KTN5,J3KSS9,A0N0Q0;UNIPARC=UPI0000001C2F;INTRON=2/2;HGVSc=ENST00000246657.2:c.61-91del;AFR_AF=0;AMR_AF=0;EAS_AF=0.004;EUR_AF=0;SAS_AF=0;MAX_AF=0.004;MAX_AF_POPS=EAS	MODIFIER	-1	CCR7	HGNC	1608	protein_coding	YES	CCDS11369.1	ENSP00000246657	P32248	UPI0000001C2F	2/2	ENST00000246657.2:c.61-91del	0	0	0.004	0	0	0.004	EAS	J3KTN5,J3KSS9,A0N0Q0													TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01
0/0	2			22		22,0	22.0	22.0	0.0	0/1	2			15		9,6	15.0			50	PASS	ATP9A	10079	.	GRCh37	20	50342307	50342308	+	Intron	DEL	TC	TC	-	novel		TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	TC	TC																c.327+50_327+51del			ENST00000338821								ATP9A,intron_variant,,ENST00000311637,;ATP9A,intron_variant,,ENST00000338821,NM_006045.1;ATP9A,intron_variant,,ENST00000402822,;ATP9A,downstream_gene_variant,,ENST00000477492,;,regulatory_region_variant,,ENSR00001644001,;	-	ENSG00000054793	ENST00000338821	Transcript	intron_variant							1		-1	ATP9A	HGNC	13540	protein_coding	YES	CCDS33489.1	ENSP00000342481	O75110	Q2NLD0,B4DR18	UPI000004D334	NM_006045.1				3/27																		MODIFIER	1	deletion														PASS	TTTCT	.	50																					50342306	20_50342307_TC/-	20:50342307-50342308	-	ENSG00000054793	ENST00000338821.5	Transcript	intron_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=-1;SYMBOL=ATP9A;SYMBOL_SOURCE=HGNC;HGNC_ID=13540;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS33489.1;ENSP=ENSP00000342481;SWISSPROT=O75110;TREMBL=Q2NLD0,B4DR18;UNIPARC=UPI000004D334;INTRON=3/27;HGVSc=ENST00000338821.5:c.327+50_327+51del	MODIFIER	-1	ATP9A	HGNC	13540	protein_coding	YES	CCDS33489.1	ENSP00000342481	O75110	UPI000004D334	3/27	ENST00000338821.5:c.327+50_327+51del								Q2NLD0,B4DR18													TCGA-A1-A0SD	TCGA-A1-A0SD-01A-11D-A10Y-09	TCGA-A1-A0SD-10A-01D-A110-09	01