"gnomad_allele" field in new VEP
1
1
Entering edit mode
20 months ago
ori.inbar ▴ 10

Hi,

Old version of VEP had the "gnomad_allele" field.

Where is this data in the current version of VEP?

Is it always the "variant_allele"?

alternatively is it the first data-set under "frequencies"

e.g. "A" in this example:

  "frequencies": {
                    "A": {

Thank you

VEP gnomad • 394 views
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4
Entering edit mode
20 months ago

Is this with a REST endpoint? Given this REST input, here's what I get under frequencies:

frequencies: {
  G: {
    eur: 0.4115,
    gnomad_amr: 0.7196,
    gnomad_oth: 0.5002,
    gnomad_afr: 0.8451,
    gnomad_asj: 0.44,
    afr: 0.9032,
    gnomad_eas: 0.8388,
    aa: 0.8268,
    ea: 0.4258,
    gnomad_nfe: 0.4197,
    gnomad_sas: 0.6202,
    gnomad_fin: 0.441,
    sas: 0.636,
    eas: 0.8532,
    gnomad: 0.5481,
    amr: 0.6354
    }
}

Since all of these frequencies are listed under the key G then they are the frequencies of the G allele. I can confirm this by going to the population genetics web-page for the same variant.

This, to me, is much clearer than the older version, where there were multiple keys for the allele, and you had to find the frequency and the allele it matched to separately. It also said things that were outright wrong like population_maf = number >0.5 – that's not a maf that's an af:

{
aa_maf: 0.8268,
gnomad_nfe_maf: 0.4202,
ea_maf: 0.4258,
gnomad_nfe_allele: "G",
gnomad_afr_maf: 0.8485,
eas_allele: "G",
amr_maf: 0.6354,
id: "rs699",
sas_allele: "G",
sas_maf: 0.636,
amr_allele: "G",
minor_allele_freq: 0.2949,
gnomad_eas_maf: 0.8378,
gnomad_fin_maf: 0.4394,
gnomad_oth_maf: 0.5164,
eas_maf: 0.8532,
gnomad_fin_allele: "G",
gnomad_eas_allele: "G",
end: 230710048,
eur_allele: "G",
gnomad_sas_maf: 0.6204,
gnomad_asj_allele: "G",
ea_allele: "G",
minor_allele: "A",
gnomad_amr_maf: 0.7185,
start: 230710048,
phenotype_or_disease: 1,
seq_region_name: 1,
gnomad_amr_allele: "G",
gnomad_sas_allele: "G",
gnomad_asj_maf: 0.4391,
strand: 1,
gnomad_maf: 0.5464,
aa_allele: "G",
allele_string: "A/G",
gnomad_oth_allele: "G",
afr_allele: "G",
afr_maf: 0.9032,
clin_sig: "benign,risk_factor",
eur_maf: 0.4115,
gnomad_allele: "G",
gnomad_afr_allele: "G",
pubmed: "deleted for clarity"
}
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