variant-population-frequency

name	variant-population-frequency
description	Query gnomAD for variant allele frequency across populations. Uses FAVOR to convert rsID→variant_id first, then queries gnomAD.
license	MIT license
metadata	{"skill-author":"PJLab"}

gnomAD Population Frequency

Usage

Tool Description

Step 1: Query FAVOR to convert rsID → chr-pos-ref-alt format.
API: GET https://api.genohub.org/v1/rsids/{rs_id}
Step 2: Query gnomAD GraphQL API with the variant_id.
API: POST https://gnomad.broadinstitute.org/api (GraphQL)
Args:
    rs_id (str): dbSNP rsID (e.g. "rs7412")
Return:
    Overall AF, population-specific AF (exome + genome), homozygote counts.

Query Example

import requests

rs_id = "rs7412"

# ── Step 1: FAVOR 获取 variant_id (chr-pos-ref-alt) ──
# 注意：FAVOR 可能返回多个变异（多等位基因位点），需遍历所有结果
favor_url = f"https://api.genohub.org/v1/rsids/{rs_id}"
favor_resp = requests.get(favor_url, timeout=30).json()
if not isinstance(favor_resp, list):
    favor_resp = [favor_resp]

variant_ids = [item.get("variant_vcf", )  item  favor_resp  item.get()]
()


query = 

 variant_vcf  variant_ids:
    ()
    resp = requests.post(
        ,
        json={: query, : {: variant_vcf}},
        timeout=
    ).json()

    v = resp.get(, {}).get(, {})
      v:
        ()
        
    ()

     source  [, ]:
        d = v.get(source, {})
         d:
            ()
             pop  (d.get()  []):
                 pop.get(, ) > :
                    af = pop[] / pop[]
                    ()