1
2
3
4
5
|
##fileformat=VCFv4.2
##contig=<ID=1,length=249250621>
##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|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|Grantham|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|IncompletePenetrance|InheritanceModesGene|VKGL|VKGL_CL|gnomAD_AF|gnomAD_COV|gnomAD_FAF95|gnomAD_FAF99|gnomAD_HN|gnomAD_QC|gnomAD_SRC|clinVar_CLNID|clinVar_CLNREVSTAT|clinVar_CLNSIG|clinVar_CLNSIGINCL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|ALPHSCORE|ncER|phyloP">
#CHROM POS ID REF ALT QUAL FILTER INFO
1 48565192 . GGTACCCGCTCTGCAGGTAGGGCAGGGTGTGCTGGGAGCAGTGGCTGCTGGCCCCGGGGCAAGGTGGGCAGCACTGATTTCCACTGTGTGCACACAGTGCCCATGCGTGTGCCCTGCATGCAGACCCTACGTGCTTGGCGTGTGCCCTGCATTCATGGACACCCATGTGCGTGTCTCGGCCCCACCCATAGCTGCCCCACGGGTTCAGCTGTCCTCACCTTCC G . PASS CSQ=-|splice_acceptor_variant&splice_donor_variant&frameshift_variant&stop_lost&splice_donor_5th_base_variant&intron_variant|HIGH|COL7A1|1294|Transcript|NM_000094.4|protein_coding|116-117/119|116/118|NM_000094.4:c.8523_8536del|NP_000085.1:p.Glu2841AspfsTer3|8586-8599/9231|8523-8536/8835|2841-2846/2944|EEGEDS*TRGAAMGGAETRTWVSMNAGHTPST*GLHAGHTHGHCVHTVEISAAHLAPGPAATAPSTPCPTCRAGTX/DX|gaGGAAGGTGAGGACAGCTGAACCCGTGGGGCAGCTATGGGTGGGGCCGAGACACGCACATGGGTGTCCATGAATGCAGGGCACACGCCAAGCACGTAGGGTCTGCATGCAGGGCACACGCATGGGCACTGTGTGCACACAGTGGAAATCAGTGCTGCCCACCTTGCCCCGGGGCCAGCAGCCACTGCTCCCAGCACACCCTGCCCTACCTGCAGAGCGGGTACcc/gacc||1||-1||1|EntrezGene||||||||||||||||||||||||||||VUS|0.5681088|||||||AD&AR||||||||||||||4|1A_(cf_Gene_count%2C_RE_gene%2C_+0.00)%3B2E-1_(COL7A1%2C_+0.90)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0.9||99.7739|,-|upstream_gene_variant|MODIFIER|PFKFB4|5210|Transcript|NM_001317136.2|protein_coding|||||||||||1|4064|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.5681742|||||||||||||||||||||||||99.7739|,-|upstream_gene_variant|MODIFIER|UCN2|90226|Transcript|NM_033199.4|protein_coding|||||||||||1|1412|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.5681742|||||||||||||||||||||||||99.7739|
|
