TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.indel.capture.tcga.txt 10.7 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
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
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	PASS	GATCT	.	50																					147121629
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	PASS	AAACA	rs112208190	50																					184043925
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
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
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	PASS	GGT	.	50																					49431403
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												PASS	ACAA	.	50																					33332313
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	PASS	TCTT	.	50																					38712160
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