Question: ensembl VEP: gnomAD genome annotation <AF1>&<AF2>
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gravatar for c.clarido
5 weeks ago by
c.clarido50
Netherlands/Rotterdam/Leiden University (Applied Science)
c.clarido50 wrote:

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 ?

ensembl gnomad vep annotation • 135 views
ADD COMMENTlink written 5 weeks ago by c.clarido50

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Pierre Lindenbaum122k

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">
ADD REPLYlink written 5 weeks ago by c.clarido50

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 ?

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum122k
##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

ADD REPLYlink written 5 weeks ago by c.clarido50

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

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum122k

yes sir: rs868804354

ADD REPLYlink written 5 weeks ago by c.clarido50

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...

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Pierre Lindenbaum122k
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