Availability of information on genes in Gnomad VCF data

Question

[Eliza]

Hi , Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the genomic location available also: exome/intron..... , if yes then what are the columns that contain this data? is it the INFO column?

thank you:)

Answer 1

[Jeremy Leipzig]

Yes they do include the VEP annotations in gnomAD as a courtesy. This is not really the point of gnomAD - the allele frequencies are the point. VEP will tell you if something is in an exon, a cds, an intron, etc... It won't really tell you the nearest gene or much at all if it's intergenic. This will all be crammed into a ridiculously hyper-serialized part of the INFO field called vep=

##INFO=<ID=vep,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|ALLELE_NUM|DISTANCE|STRAND|VARIANT_CLASS|MINIMISED| 
SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO| 
SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE| 
LoF|LoF_filter|LoF_flags|LoF_info">

[Eliza]

Thank you very much,is the vep I the info column ? can maybe the nearest gene be: gene-STRING-Corresponding gene name of the highly affected transcript? And maybe do you know were I can get the information about the nearest gene to an SNP , if not in gnomad ?

[Jeremy Leipzig]

if you have your own VCF then you should annotate it using VEP and --plugin NearestGene https://uswest.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#nearestgene

as you mentioned some variants are not even in gnomAD

[Eliza]

Thank you just to make sure the VEP in info column will give me the location exone ,cdc,intron ,,,,,