ensembl VEP: gnomAD genome annotation <AF1>&<AF2>

Question

[c.clarido]

Hello community,

CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|AL627309.1|ENSG00000238009|Transcript|ENST00000466430|lincRNA||2/3||||||||||-1||Clone_based_ensembl_gene||||||||||||||||||||||1:96806-96806|0.0024263|1:96806-96806&rs868804354|3.31236e-05&7.19867e-02,T|intron_variant&non_coding_transcript_variant|MODIFIER|AL627309.1|ENSG00000238009|Transcript|ENST00000477740|lincRNA||3/3||||||||||-1||Clone_based_ensembl_gene||||||||||||||||||||||1:96806-96806|0.0024263|1:96806-96806&rs868804354|3.31236e-05&7.19867e-02

Here I have a CSQ field of a variant. What does '&' mean here: 3.31236e-05&7.19867e-02,T ?

[Pierre Lindenbaum]

what is the definition header for INFO=<ID=CSQ ? what are the column corresponding to your annotation ?

[c.clarido]

I'm sorry, I don't understand what you mean. Do you perhaps mean this?:

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene.....|goNl|goNl_AF|kaviar|kaviar_AF|gnomAD|gnomAD_AF">

[Pierre Lindenbaum]

yes (my messsage was messed-up by the biostar engine) , what is the column in the header corresponding to 3.31236e-05&7.19867e-02 ?

[c.clarido]

##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|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|SOURCE|GENE_PHENO|DOMAINS|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|CADD_phred|FATHMM_pred|M-CAP_pred|MetaSVM_pred|MutationAssessor_pred|Polyphen2_HDIV_pred|Polyphen2_HVAR_pred|SIFT_pred|gnomAD_genomes_AF|phastCons100way_vertebrate|phyloP100way_vertebrate|goNl|goNl_AF|kaviar|kaviar_AF|gnomAD|gnomAD_AF">

It is the gnomAD_AF I don't understand the format: AF1&AF2,T

[Pierre Lindenbaum]

is it this variant ? https://gnomad.broadinstitute.org/variant/1-96806-C-T

[c.clarido]

yes sir: rs868804354

[Pierre Lindenbaum]

I would have say that there are two alternative alleles at this position, or two values for genomes and exomes, but I don't even find the same AF values at that position in gnomad...