1
2
3
4
5
6
7
|
##fileformat=VCFv4.2
##contig=<ID=chrX,length=156040895>
##VEP="v102" time="2020-12-14 19:43:49" cache="/opt/vep/.vep/homo_sapiens/102_GRCh38" ensembl-variation=102.2716d2e ensembl-io=102.ff1cf96 ensembl-funcgen=102.6bd93a0 ensembl=102.347f9ed 1000genomes="phase3" COSMIC="91" ClinVar="202006" ESP="V2-SSA137" HGMD-PUBLIC="20194" assembly="GRCh38.p13" dbSNP="153" gencode="GENCODE 36" genebuild="2014-07" 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|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|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|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceRegion|GeneSplicer|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|CADD_PHRED|CADD_RAW|LoF|LoF_filter|LoF_flags|LoF_info|REVEL|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">
#CHROM POS ID REF ALT QUAL FILTER INFO
chrX 41334153 . G A . . CSQ=A|5_prime_UTR_variant&NMD_transcript_variant|MODIFIER|DDX3X|ENSG00000215301|Transcript|ENST00000478993|nonsense_mediated_decay|1/19||ENST00000478993.5:c.-100G>A||756||||||1||1||SNV|HGNC|HGNC:2745|||1||CCDS43931.1|ENSP00000478443|O00571.228||UPI000013CB6D|O00571-1|1|||||||||||||||||||||||||||||||||||loss/donor/41334153-41334154/Medium/1.787081|0|0|2|uAUG_gained_CapDistanceToStart:755&uAUG_gained_DistanceToCDS:100&uAUG_gained_DistanceToStop:27&uAUG_gained_KozakContext:GCGATGC&uAUG_gained_KozakStrength:Moderate&uAUG_gained_type:uORF|uAUG_gained|15.55|1.471728||||||-27|11|-27|-25|0.01|0.00|0.00|0.00|DDX3X
chrX 41334585 . GGACGCGCATGCGC G . . CSQ=-|intron_variant|MODIFIER|DDX3X|ENSG00000215301|Transcript|ENST00000457138|protein_coding||1/15|ENST00000457138.7:c.45+291_45+303del||||||||1||1||deletion|HGNC|HGNC:2745|||2||CCDS55404.1|ENSP00000392494|O00571.228||UPI00017A8655|O00571-2|1||||||||||||||||||||||||||||||||||||||||||||||||||||||||,-|intron_variant&NMD_transcript_variant|MODIFIER|DDX3X|ENSG00000215301|Transcript|ENST00000478993|nonsense_mediated_decay||1/18|ENST00000478993.5:c.45+291_45+303del||||||||1||1||deletion|HGNC|HGNC:2745|||1||CCDS43931.1|ENSP00000478443|O00571.228||UPI000013CB6D|O00571-1|1||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
