TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.indel.capture.tcga.vep.vcf 31.4 KB
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##fileformat=VCFv4.1
##fileDate=20160402
##tcgaversion=1.1
##reference=<ID=hg19,source="http://www.broadinstitute.org/ftp/pub//seq/references/Homo_sapiens_assembly19.fasta">
##assembly=.
##center="broad.mit.edu"
##phasing=none
##geneAnno=http://www.gencodegenes.org/
##vcfProcessLog=<InputVCF=<.>,InputVCFSource=<.>,InputVCFVer=<.>,InputVCFParam=<.>,InputVCFgeneAnno=<https://tcga-data.nci.nih.gov/docs/GAF/GAF3.0/>>
##INDIVIDUAL=TCGA-A1-A0SB
##SAMPLE=<ID=NORMAL,SampleTCGABarcode=TCGA-A1-A0SB-10B-01D-A142-09,SampleName=TCGA-A1-A0SB-10B-01D-A142-09,Individual=TCGA-A1-A0SB,Description="Normal sample",Platform=Illumina,Source=dbGaP,Accession=.,softwareName=<muTect,CallIndelsPipeline>,softwareVer=<119,65>,softwareParam=<.>,File=TCGA-A1-A0SB-10B-01D-A142-09,SampleUUID=a3254f8e-3bbd-42fc-abea-a5f25b7648b3,MetadataResource=https://tcga-data.nci.nih.gov/uuid/uuidws/mapping/xml/uuid/a3254f8e-3bbd-42fc-abea-a5f25b7648b3>
##SAMPLE=<ID=PRIMARY,SampleTCGABarcode=TCGA-A1-A0SB-01A-11D-A142-09,SampleName=TCGA-A1-A0SB-01A-11D-A142-09,Individual=TCGA-A1-A0SB,Description="Primary Tumor",Platform=Illumina,Source=dbGaP,Accession=.,softwareName=<muTect,CallIndelsPipeline>,softwareVer=<119,65>,softwareParam=<.>,File=TCGA-A1-A0SB-01A-11D-A142-09,SampleUUID=db9d40fb-bfce-4c3b-a6c2-41c5c88982f1,MetadataResource=https://tcga-data.nci.nih.gov/uuid/uuidws/mapping/xml/uuid/db9d40fb-bfce-4c3b-a6c2-41c5c88982f1>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Depth of reads supporting alleles 0/1/2/3...">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=FA,Number=.,Type=Float,Description="Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample">
##FORMAT=<ID=MQ0,Number=1,Type=Integer,Description="Number of Mapping Quality Zero Reads per sample">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality for reads supporting alleles">
##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic score between 0 and 255">
##INFO=<ID=Gene,Number=1,Type=String,Description="Hugo Gene Symbol">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=VC,Number=1,Type=String,Description="Somatic variant classification">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of sample">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth across samples">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=TID,Number=1,Type=String,Description="Transcript ID">
##INFO=<ID=VLSC,Number=1,Type=Integer,Description="Final somatic score between 0 and 255 when multiple lines of evidence are available">
##FILTER=<ID=mf1,Description="Filtered out by MuTect v.1">
##FILTER=<ID=oxoG3,Description="Filtered out by OxoG Artifact Filter v3">
##VEP="v102" time="2021-02-14 10:37:51" cache="/Users/ypradat/.vep/homo_sapiens/101_GRCh37" ensembl-io=101.943b6c2 ensembl=101.856c8e8 ensembl-variation=101.851c7e0 ensembl-funcgen=101.b918a49 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|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|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	PRIMARY
1	16386305	rs143272992	G	GC	50	PASS	DB;DP=17;Gene=FAM131C;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=INS;TID=ENST00000375662.4;VLSC=255;CSQ=C|intron_variant|MODIFIER|FAM131C|ENSG00000185519|Transcript|ENST00000375662|protein_coding||5/6|ENST00000375662.4:c.451+58dup|||||||rs372070031|1||-1||1|insertion|HGNC|26717|YES||CCDS41270.1|ENSP00000364814|Q96AQ9||UPI000022B016||NM_182623.2|||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000375667|protein_coding||||||||||rs372070031|1|2502|1|||insertion|HGNC|2027|||CCDS57974.1|ENSP00000364819|P51801||UPI000046FF10||NM_001165945.2|1||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000375679|protein_coding||||||||||rs372070031|1|2502|1|||insertion|HGNC|2027|YES||CCDS168.1|ENSP00000364831|P51801||UPI000040E261||NM_000085.4|1||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000431772|protein_coding||||||||||rs372070031|1|2502|1|cds_start_NF||insertion|HGNC|2027||||ENSP00000389344||Q5T5Q6|UPI000046FF11|||1||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|FAM131C|ENSG00000185519|Transcript|ENST00000494078|processed_transcript||4/5|ENST00000494078.1:n.525+58dup|||||||rs372070031|1||-1|||insertion|HGNC|26717||||||||||||||||0.2731|0.3573|0.3581|0.3757|0.5051||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:11,0:11:0.000:0:.:2:.	0/1:4,2:6:0.333:0:.:2:.
3	147121629	.	ATC	A	50	PASS	DP=12;Gene=ZIC4;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=DEL;TID=ENST00000491672.1;VLSC=255;CSQ=-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000383075|protein_coding||1/4|ENST00000383075.3:c.-15-1032_-15-1031del|||||||rs142316820|1||-1|||deletion|HGNC|20393|||CCDS43160.1|ENSP00000372553|Q8N9L1|C9JZU7&C9JD04&C9J6T3&B3KPI4|UPI000013F1E0||NM_032153.5|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000425731|protein_coding||1/4|ENST00000425731.3:c.100-1032_100-1031del|||||||rs142316820|1||-1|||deletion|HGNC|20393|||CCDS54653.1|ENSP00000397695|Q8N9L1|C9JZU7&C9JD04&C9J6T3&B3KPI4|UPI0001AE75DF||NM_001168379.1|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000462748|protein_coding||1/2|ENST00000462748.2:c.-15-1032_-15-1031del|||||||rs142316820|1||-1|cds_end_NF||deletion|HGNC|20393||||ENSP00000420627||C9JZU7&C9JD04&C9J6T3|UPI0001B79697|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000463250|protein_coding||2/3|ENST00000463250.1:c.-15-1032_-15-1031del|||||||rs142316820|1||-1|cds_end_NF||deletion|HGNC|20393||||ENSP00000419727||C9JZU7|UPI0001B79699|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000464144|processed_transcript||||||||||rs142316820|1|1608|-1|||deletion|HGNC|20393||||||||||1||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ZIC1|ENSG00000152977|Transcript|ENST00000472523|processed_transcript||1/1|ENST00000472523.1:n.521+9917_521+9918del|||||||rs142316820|1||1|||deletion|HGNC|12872||||||||||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000473123|protein_coding||1/4|ENST00000473123.1:c.-15-1032_-15-1031del|||||||rs142316820|1||-1|||deletion|HGNC|20393|||CCDS43160.1|ENSP00000420775|Q8N9L1|C9JZU7&C9JD04&C9J6T3&B3KPI4|UPI000013F1E0|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000484399|protein_coding||1/4|ENST00000484399.1:c.-16+120_-16+121del|||||||rs142316820|1||-1|||deletion|HGNC|20393|||CCDS43160.1|ENSP00000417855|Q8N9L1|C9JZU7&C9JD04&C9J6T3&B3KPI4|UPI000013F1E0|||1||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000484586|protein_coding||||||||||rs142316820|1|45|-1|cds_end_NF||deletion|HGNC|20393||||ENSP00000418343||C9JZU7&C9J6T3|UPI0001B79698|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC1|ENSG00000152977|Transcript|ENST00000488404|protein_coding||1/2|ENST00000488404.1:c.49-8659_49-8658del|||||||rs142316820|1||1|cds_start_NF||deletion|HGNC|12872||||ENSP00000419664|||UPI0001B7969A|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000491672|protein_coding||1/3|ENST00000491672.1:c.-15-1032_-15-1031del|||||||rs142316820|1||-1|||deletion|HGNC|20393|||CCDS58857.1|ENSP00000418277|Q8N9L1||UPI0001B79696||NM_001243256.1|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ZIC4|ENSG00000174963|Transcript|ENST00000525172|protein_coding||1/4|ENST00000525172.2:c.135+120_135+121del|||||||rs142316820|1||-1||1|deletion|HGNC|20393|YES||CCDS54652.1|ENSP00000435509|Q8N9L1|C9JZU7&C9JD04&C9J6T3&B3KPI4|UPI0001914D88||NM_001168378.1|1||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:6,0:6:0.000:0:.:2:.	0/1:4,2:6:0.333:0:.:2:.
3	184043925	rs112208190	AAC	A	50	PASS	DB;DP=13;Gene=EIF4G1;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=DEL;TID=ENST00000392537.2;VLSC=255;CSQ=-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000319274|protein_coding||20/31|ENST00000319274.6:c.3222+217_3222+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS3259.1|ENSP00000323737|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9JIH5&C9J987&C9J6B6&C9J556|UPI00003671E5|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000342981|protein_coding||20/31|ENST00000342981.4:c.3225+217_3225+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS54688.1|ENSP00000343450|Q04637|Q96I65&E9PGM1&E7EX73&E7EUU4&C9JWW9&C9JWH7&C9JSU8&C9JIH5&C9J987&C9J556&C9J2Z7|UPI000014054E||NM_182917.4|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000346169|protein_coding||21/32|ENST00000346169.2:c.3222+217_3222+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS3259.1|ENSP00000316879|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9JIH5&C9J987&C9J6B6&C9J556|UPI00003671E5||NM_198241.2|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000350481|protein_coding||17/28|ENST00000350481.5:c.2730+217_2730+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS3261.1|ENSP00000317600|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J6B6&C9J556|UPI000021BFAF||NM_198242.2|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000352767|protein_coding||21/32|ENST00000352767.3:c.3243+217_3243+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS54687.1|ENSP00000338020|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J987&C9J6B6&C9J556|UPI00015E0966||NM_001194947.1|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000382330|protein_coding||22/33|ENST00000382330.3:c.3243+217_3243+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS54687.1|ENSP00000371767|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J987&C9J6B6&C9J556|UPI00015E0966||NM_001194946.1|1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|SNORD66|ENSG00000212158|Transcript|ENST00000390856|snoRNA||||||||||rs34901174|1|367|1|||deletion|HGNC|32727|YES||||||||NR_003055.1|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000392537|protein_coding||18/29|ENST00000392537.2:c.2961+217_2961+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS3260.1|ENSP00000376320|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J987&C9J6B6&C9J556|UPI00003671E6||NM_198244.2|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000411531|protein_coding||18/29|ENST00000411531.1:c.3105+217_3105+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||ENSP00000395974||Q96I65&E9PGM1&E7EX73&E7EUU4&C9JWW9&C9JWH7&C9JSU8&C9JIH5&C9J987&C9J556|UPI000198CBBE|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000413967|nonsense_mediated_decay||||||||||rs34901174|1|839|1|||deletion|HGNC|3296||||ENSP00000390755||F8WB97|UPI000198CBA2|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000414031|protein_coding||21/32|ENST00000414031.1:c.3102+217_3102+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||ENSP00000391935|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9JIH5&C9J987&C9J6B6&C9J556|UPI000198CBA8|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000421110|protein_coding||||||||||rs34901174|1|1826|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000413159||C9K073&C9JWW9&C9JWH7&C9JSU8&C9J987&C9J556|UPI000198CBA4|||1||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000422614|nonsense_mediated_decay||||||||||rs34901174|1|1810|1|cds_start_NF||deletion|HGNC|3296||||ENSP00000396888|||UPI000198CBB4|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000424196|protein_coding||20/31|ENST00000424196.1:c.3243+217_3243+218del|||||||rs34901174|1||1||1|deletion|HGNC|3296|YES||CCDS54687.1|ENSP00000416255|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J987&C9J6B6&C9J556|UPI00015E0966|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000426123|protein_coding||||||||||rs34901174|1|839|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000403269||C9JWW9&C9JWH7&C9JSU8&C9JF13&C9J6B6&C9J556|UPI000198CBA3|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000427607|protein_coding||||||||||rs34901174|1|4477|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000409545||C9JWH7&C9JSU8&C9J556|UPI000198CBB1|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000427845|protein_coding||18/29|ENST00000427845.1:c.2964+217_2964+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||ENSP00000407682||Q96I65&E9PGM1&E7EX73&C9JWW9&C9JWH7&C9JSU8&C9J987&C9J556|UPI000198CBA9|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000428387|protein_coding||||||||||rs34901174|1|4535|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000411707||C9JWH7&C9J556|UPI000198CBB0|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000434061|protein_coding||14/25|ENST00000434061.2:c.2637+217_2637+218del|||||||rs34901174|1||1|||deletion|HGNC|3296|||CCDS46970.2|ENSP00000411826|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J556|UPI0000E5AB2D||NM_004953.4|1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000435046|protein_coding||14/25|ENST00000435046.2:c.2634+217_2634+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||ENSP00000404754|Q04637|Q96I65&C9JWW9&C9JWH7&C9JSU8&C9J556|UPI000021BFAD|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000441154|protein_coding||15/26|ENST00000441154.1:c.2733+217_2733+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||ENSP00000399858||Q96I65&E7EX73&C9JWW9&C9JWH7&C9JSU8&C9J556|UPI000198CBBF|||1||||||||||||||||||||||||||||||,-|intron_variant&NMD_transcript_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000442406|nonsense_mediated_decay||17/28|ENST00000442406.1:c.*2661+217_*2661+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||ENSP00000400351||F8WCF2|UPI000198CB9F|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000444134|protein_coding||||||||||rs34901174|1|4584|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000407244||C9JWH7|UPI000198CBB5|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF2B5|ENSG00000145191|Transcript|ENST00000444495|protein_coding||15/15|ENST00000444495.1:c.2106+181461_2106+181462del|||||||rs34901174|1||1|||deletion|HGNC|3261||||ENSP00000409142||E9PC74&C9JRD9|UPI0001892643|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000444861|protein_coding||||||||||rs34901174|1|1117|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000398145||C9JWW9&C9JWH7&C9JSU8&C9J6B6&C9J556|UPI000198CBAB|||1||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000448284|protein_coding||4/6|ENST00000448284.1:c.383+211_383+212del|||||||rs34901174|1||1|cds_start_NF&cds_end_NF||deletion|HGNC|3296||||ENSP00000392908|||UPI000198CBB3|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000450424|protein_coding||||||||||rs34901174|1|1912|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000391412||C9JWW9&C9JWH7&C9JSU8&C9JIH5&C9J987&C9J556&C9J2Z7|UPI000198CBA5|||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000457456|protein_coding||||||||||rs34901174|1|4111|1|cds_end_NF||deletion|HGNC|3296||||ENSP00000399969||C9JWW9&C9JWH7&C9JSU8&C9J556|UPI000198CBB2|||1||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000460829|retained_intron||||||||||rs34901174|1|1978|1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000464548|retained_intron||||||||||rs34901174|1|2530|1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000466311|retained_intron||2/3|ENST00000466311.1:n.442+217_442+218del|||||||rs34901174|1||1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000475721|retained_intron||||||||||rs34901174|1|2477|1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000482303|retained_intron||||||||||rs34901174|1|1147|1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000484862|retained_intron||||||||||rs34901174|1|4604|1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|EIF4G1|ENSG00000114867|Transcript|ENST00000493299|retained_intron||||||||||rs34901174|1|4631|1|||deletion|HGNC|3296||||||||||1||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:7,0:7:0.000:0:.:2:.	0/1:2,4:6:0.667:0:.:2:.
7	22533451	rs116873396	TCA	T	50	PASS	DB;DP=28;Gene=STEAP1B;MQ0=0;SOMATIC;SS=Somatic;VC=Frame_Shift_Del;VT=DEL;TID=ENST00000404369.4;VLSC=255;CSQ=-|frameshift_variant&splice_region_variant|HIGH|STEAP1B|ENSG00000105889|Transcript|ENST00000404369|protein_coding|3/5||ENST00000404369.4:c.87_88del|ENSP00000384370.4:p.His29GlnfsTer24|503-504/1515|87-88/1029|29-30/342|HE/QX|caTGag/caag||1||-1||1|deletion|HGNC|41907|YES||CCDS56469.1|ENSP00000384370||C9JL51&C9JE84&B5MCI2|UPI000173A267||NM_001164460.1||||PANTHER:PTHR14239:SF3&PANTHER:PTHR14239|||||||||||||||||||||||||||,-|intron_variant|MODIFIER|STEAP1B|ENSG00000105889|Transcript|ENST00000406890|protein_coding||2/4|ENST00000406890.2:c.85-55_85-54del||||||||1||-1|||deletion|HGNC|41907|||CCDS55094.1|ENSP00000385239|Q6NZ63||UPI000023C86C||NM_207342.2|||||||||||||||||||||||||||||||,-|frameshift_variant&splice_region_variant|HIGH|STEAP1B|ENSG00000105889|Transcript|ENST00000424363|protein_coding|4/5||ENST00000424363.1:c.87_88del|ENSP00000416608.1:p.His29GlnfsTer24|329-330/1004|87-88/762|29-30/254|HE/QX|caTGag/caag||1||-1|cds_end_NF||deletion|HGNC|41907||||ENSP00000416608||C9JL51&C9JE84&A4D137|UPI0000246BB7||||||PANTHER:PTHR14239:SF3&PANTHER:PTHR14239|||||||||||||||||||||||||||,-|frameshift_variant&splice_region_variant|HIGH|STEAP1B|ENSG00000105889|Transcript|ENST00000439708|protein_coding|3/4||ENST00000439708.1:c.87_88del|ENSP00000408954.1:p.His29GlnfsTer24|234-235/797|87-88/650|29-30/216|HE/QX|caTGag/caag||1||-1|cds_end_NF||deletion|HGNC|41907||||ENSP00000408954||C9JL51|UPI000188145E||||||PANTHER:PTHR14239&PANTHER:PTHR14239:SF3|||||||||||||||||||||||||||,-|splice_region_variant&non_coding_transcript_exon_variant|LOW|STEAP1B|ENSG00000105889|Transcript|ENST00000483679|retained_intron|3/4||ENST00000483679.1:n.206_207del||206-207/1054||||||1||-1|||deletion|HGNC|41907||||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:22,0:22:0.000:0:.:2:.	0/1:4,2:6:0.333:0:.:2:.
11	112042479	.	CT	C	50	PASS	DP=37;Gene=TEX12;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=DEL;TID=ENST00000280358.4;VLSC=255;CSQ=-|intron_variant|MODIFIER|TEX12|ENSG00000150783|Transcript|ENST00000280358|protein_coding||4/4|ENST00000280358.4:c.228-9del|||||||rs1225064086|1||1||1|deletion|HGNC|11734|YES||CCDS31679.1|ENSP00000280358|Q9BXU0||UPI00001377E3||NM_031275.4||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000357685|protein_coding||||||||||rs1225064086|1|3710|1|||deletion|HGNC|18503|YES||CCDS8358.2|ENSP00000350314|Q9BYV7|E9PS89&B0YIX6|UPI00005FB124||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000361053|protein_coding||||||||||rs1225064086|1|3765|1|||deletion|HGNC|18503|||CCDS58181.1|ENSP00000354338|Q9BYV7|E9PS89&B0YIX7|UPI00015E0029||NM_001256398.1||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000393032|protein_coding||||||||||rs1225064086|1|3728|1|||deletion|HGNC|18503|||CCDS41716.1|ENSP00000376752|Q9BYV7||UPI000013D0B9||NM_031938.5||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000438022|protein_coding||||||||||rs1225064086|1|3999|1|||deletion|HGNC|18503|||CCDS41716.1|ENSP00000414843|Q9BYV7||UPI000013D0B9||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000460924|retained_intron||||||||||rs1225064086|1|3753|1|||deletion|HGNC|18503|||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000461480|retained_intron||||||||||rs1225064086|1|3755|1|||deletion|HGNC|18503|||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000494860|retained_intron||||||||||rs1225064086|1|3788|1|||deletion|HGNC|18503|||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|SDHD|ENSG00000255292|Transcript|ENST00000525468|processed_transcript||3/3|ENST00000525468.1:n.282+1233del|||||||rs1225064086|1||1|||deletion|Uniprot_gn||||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|SDHD|ENSG00000255292|Transcript|ENST00000525987|retained_intron||4/5|ENST00000525987.1:n.431+1233del|||||||rs1225064086|1||1|||deletion|Uniprot_gn||||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000526088|protein_coding||||||||||rs1225064086|1|4614|1|||deletion|HGNC|18503|||CCDS58182.1|ENSP00000436615|Q9BYV7||UPI0001E24F15||NM_001037290.2&NM_001256397.1||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-356J5.4|ENSG00000254638|Transcript|ENST00000527589|antisense||1/3|ENST00000527589.1:n.52+798del|||||||rs1225064086|1||-1|||deletion|Clone_based_vega_gene||YES||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000527939|nonsense_mediated_decay||||||||||rs1225064086|1|3789|1|||deletion|HGNC|18503||||ENSP00000436956||E9PPP9|UPI0001F78245||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant|MODIFIER|TEX12|ENSG00000150783|Transcript|ENST00000530752|protein_coding||4/4|ENST00000530752.1:c.228-9del|||||||rs1225064086|1||1|||deletion|HGNC|11734|||CCDS31679.1|ENSP00000436893|Q9BXU0||UPI00001377E3||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000531003|nonsense_mediated_decay||||||||||rs1225064086|1|3775|1|||deletion|HGNC|18503||||ENSP00000435869||E9PS89|UPI0001F78246||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000531169|protein_coding||||||||||rs1225064086|1|4643|1|||deletion|HGNC|18503|||CCDS41716.1|ENSP00000437053|Q9BYV7||UPI000013D0B9||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant&NMD_transcript_variant|MODIFIER|SDHD|ENSG00000255292|Transcript|ENST00000531744|nonsense_mediated_decay||5/5|ENST00000531744.1:c.*55+1089del|||||||rs1225064086|1||1|||deletion|Uniprot_gn|||||ENSP00000456957||H3BRW5&G3V173|UPI0001F781B3||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000532593|protein_coding||||||||||rs1225064086|1|4618|1|||deletion|HGNC|18503|||CCDS58183.1|ENSP00000431802|Q9BYV7||UPI0000DFFFC8||NM_001256400.1||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant|MODIFIER|AP002884.3|ENSG00000272790|Transcript|ENST00000532612|protein_coding||1/4|ENST00000532612.1:c.1+1233del|||||||rs1225064086|1||1|cds_start_NF&cds_end_NF||deletion|Clone_based_vega_gene||YES|||ENSP00000476560|||UPI0003B92884||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|intron_variant&NMD_transcript_variant|MODIFIER|SDHD|ENSG00000255292|Transcript|ENST00000532699|nonsense_mediated_decay||5/5|ENST00000532699.1:c.*55+1089del|||||||rs1225064086|1||1|||deletion|Uniprot_gn||YES|||ENSP00000456434||H3BRW5&G3V173|UPI0001F781B3||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000534122|retained_intron||||||||||rs1225064086|1|3999|1|||deletion|HGNC|18503|||||||||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||,-|upstream_gene_variant|MODIFIER|BCO2|ENSG00000197580|Transcript|ENST00000534550|nonsense_mediated_decay||||||||||rs1225064086|1|3759|1|||deletion|HGNC|18503||||ENSP00000434488||E9PPP9|UPI0001F78245||||||||||||||||1.711e-05|8.319e-05|0|0|8.285e-05|0|1.133e-05|0|0|||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:31,0:31:0.000:0:.:2:.	0/1:4,2:6:0.333:0:.:2:.
12	49431403	.	G	GT	50	PASS	DP=81;Gene=KMT2D;MQ0=0;SOMATIC;SS=Somatic;VC=Frame_Shift_Ins;VT=INS;TID=ENST00000301067.7;VLSC=255;CSQ=T|frameshift_variant|HIGH|KMT2D|ENSG00000167548|Transcript|ENST00000301067|protein_coding|34/54||ENST00000301067.7:c.9735dup|ENSP00000301067.7:p.Pro3246ThrfsTer5|9735-9736/19419|9735-9736/16614|3245-3246/5537|-/X|-/A||1||-1||1|insertion|HGNC|7133|YES||CCDS44873.1|ENSP00000301067|O14686|Q6PIA1&Q59FG6&F8VWW4|UPI0000EE84D6||NM_003482.3|1|||PANTHER:PTHR22884&PANTHER:PTHR22884:SF324|||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|KMT2D|ENSG00000167548|Transcript|ENST00000549743|processed_transcript|||||||||||1|324|-1|||insertion|HGNC|7133||||||||||1||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|KMT2D|ENSG00000167548|Transcript|ENST00000549799|processed_transcript|||||||||||1|847|-1|||insertion|HGNC|7133||||||||||1||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:48,0:48:0.000:0:.:2:.	0/1:26,7:33:0.212:0:.:2:.
13	33332313	.	CA	C	50	PASS	DP=53;Gene=PDS5B;MQ0=0;SOMATIC;SS=Somatic;VC=Frame_Shift_Del;VT=DEL;TID=ENST00000315596.10;VLSC=255;CSQ=-|frameshift_variant|HIGH|PDS5B|ENSG00000083642|Transcript|ENST00000315596|protein_coding|27/35||ENST00000315596.10:c.3148del|ENSP00000313851.10:p.Thr1050GlnfsTer12|3332/7497|3146/4344|1049/1447|Q/X|cAa/ca||1||1||1|deletion|HGNC|20418|YES||CCDS41878.1|ENSP00000313851|Q9NTI5||UPI000006D4A9||NM_015032.3||||PANTHER:PTHR12663&PANTHER:PTHR12663:SF1|2||||||||||||||||||||||||||,-|frameshift_variant|HIGH|PDS5B|ENSG00000083642|Transcript|ENST00000447833|protein_coding|1/6||ENST00000447833.1:c.10del|ENSP00000407005.1:p.Thr4GlnfsTer12|8/906|8/906|3/302|Q/X|cAa/ca||1||1|cds_start_NF&cds_end_NF||deletion|HGNC|20418||||ENSP00000407005||A9IYQ1|UPI0001611384||||||PANTHER:PTHR12663&PANTHER:PTHR12663:SF1|2||||||||||||||||||||||||||,-|frameshift_variant&NMD_transcript_variant|HIGH|PDS5B|ENSG00000083642|Transcript|ENST00000450460|nonsense_mediated_decay|27/34||ENST00000450460.1:c.3148del|ENSP00000401619.1:p.Thr1050GlnfsTer12|3211/5246|3146/4176|1049/1391|Q/X|cAa/ca||1||1|||deletion|HGNC|20418||||ENSP00000401619|Q9NTI5||UPI00001FCBD4||||||PANTHER:PTHR12663&PANTHER:PTHR12663:SF1|2||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:47,0:47:0.000:0:.:2:.	0/1:4,2:6:0.333:0:.:2:.
17	38712160	.	CT	C	50	PASS	DP=11;Gene=CCR7;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=DEL;TID=ENST00000246657.2;VLSC=255;CSQ=-|intron_variant|MODIFIER|CCR7|ENSG00000126353|Transcript|ENST00000246657|protein_coding||2/2|ENST00000246657.2:c.61-91del|||||||rs372297045|1||-1||1|deletion|HGNC|1608|YES||CCDS11369.1|ENSP00000246657|P32248|J3KTN5&J3KSS9&A0N0Q0|UPI0000001C2F||NM_001838.3|1||||||0|0|0.004|0|0||||||||||||||||||||,-|intron_variant|MODIFIER|CCR7|ENSG00000126353|Transcript|ENST00000578085|protein_coding||1/1|ENST00000578085.1:c.-129-91del|||||||rs372297045|1||-1|cds_end_NF||deletion|HGNC|1608||||ENSP00000463075||J3KTN5|UPI000268B055|||1||||||0|0|0.004|0|0||||||||||||||||||||,-|intron_variant|MODIFIER|CCR7|ENSG00000126353|Transcript|ENST00000579344|protein_coding||2/2|ENST00000579344.1:c.43-91del|||||||rs372297045|1||-1|||deletion|HGNC|1608||||ENSP00000462631||J3KTN5&J3KSS9|UPI0000200C7F|||1||||||0|0|0.004|0|0||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:5,0:5:0.000:0:.:2:.	0/1:4,2:6:0.333:0:.:2:.
20	50342306	.	TTC	T	50	PASS	DP=37;Gene=ATP9A;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=DEL;TID=ENST00000338821.5;VLSC=255;CSQ=-|intron_variant|MODIFIER|ATP9A|ENSG00000054793|Transcript|ENST00000311637|protein_coding||3/22|ENST00000311637.5:c.282+50_282+51del||||||||1||-1|||deletion|HGNC|13540||||ENSP00000309086|||UPI00004709CC|||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ATP9A|ENSG00000054793|Transcript|ENST00000338821|protein_coding||3/27|ENST00000338821.5:c.327+50_327+51del||||||||1||-1||1|deletion|HGNC|13540|YES||CCDS33489.1|ENSP00000342481|O75110|Q2NLD0&B4DR18|UPI000004D334||NM_006045.1|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ATP9A|ENSG00000054793|Transcript|ENST00000402822|protein_coding||3/22|ENST00000402822.1:c.327+50_327+51del||||||||1||-1|||deletion|HGNC|13540||||ENSP00000385875|O75110||UPI000002A425|||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ATP9A|ENSG00000054793|Transcript|ENST00000477492|processed_transcript|||||||||||1|50|-1|||deletion|HGNC|13540||||||||||||||||||||||||||||||||||||||||,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001644001||||||||||||1|||||deletion||||||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:22,0:22:0.000:0:.:2:.	0/1:9,6:15:0.400:0:.:2:.