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Question: gnomAD: query utilitites
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I wanted to query the gnomAD database without having to download and configure the entire data. Is there a way gnomAD provides an API for programmatic access? For example, for a given variant id, I want to retrieve the Total 'Allele Count':

INPUT: '1-978628-C-T' (or 'rs116586548')

i.e. if we query the website (gnomAD

I have thousands of variants that I want to get the Total Allele Count for, but would prefer not to download the entire dataset.


ADD COMMENTlink 10 months ago bsmith030465 • 140 • updated 10 months ago Garan • 570
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use an API like

wget -q -O - "" H  "accept: application/json"  
    "an": {
      "an": 30864,
      "an_afr": 8690,
      "an_amr": 838,
      "an_asj": 302,
      "an_eas": 1622,
      "an_female": 13804,
      "an_fin": 3490,
      "an_male": 17060,
      "an_nfe": 14940,
      "an_oth": 982,
      "an_popmax": 8690,
      "an_raw": 30990

ADD COMMENTlink 10 months ago Pierre Lindenbaum 120k
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I don't think so, at least not officially. You might be able to find a third party web application that has gnomAD data.

Bravo is another variant database that seems to use part of the ExAC browser codebase: and they provide an API. The data might not be as rich as gnomAD but it might be enough depending on what you need.

Varsome is a commerical variant database that might work here too: which is free with some restrictions but also provides some premium models. They provide a sample client API as well:

There's some other solutions: I couldn't get the tabix one to work though (the URL is different now, but still didn't work in my case.)

ADD COMMENTlink 10 months ago manuel.belmadani • 830
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tabix doesn't work anymore because the server for gnomad doesn't support "range-query" anymore.

ADD REPLYlink 10 months ago
Pierre Lindenbaum
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The Cellbase Swagger restful API might have what you're after, although I'm not sure how many requests it will take if you're looking to bulk query.

population  "ALL"
refAllele   "C"
altAllele   "T"
refAlleleFreq   0.99945223
altAlleleFreq   0.00054777955
refHomGenotypeFreq  0.99890447
hetGenotypeFreq 0.0010955591
altHomGenotypeFreq  0
population  "OTH"
refAllele   "C"
altAllele   "T"
refAlleleFreq   0.9998051
altAlleleFreq   0.00019493178
refHomGenotypeFreq  0.9996101
hetGenotypeFreq 0.00038986356
altHomGenotypeFreq  0
ADD COMMENTlink 10 months ago Garan • 570

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