bio-clinical-databases-gnomad-frequencies

Version Compatibility

Reference examples tested with: requests 2.31+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

gnomAD Frequency Queries

gnomAD REST API

Goal: Retrieve exome and genome allele frequencies from gnomAD for individual variants.

Approach: Send a GraphQL query to the gnomAD API with variant ID and dataset version, then parse exome/genome frequency fields.

"Check how common this variant is in the population" → Query gnomAD for allele frequency, allele count, and homozygote count.

• Python: GraphQL via requests.post() (requests)
• Python: myvariant.MyVariantInfo().getvariant() (myvariant)

Query Single Variant

import requests

def query_gnomad(chrom, pos, ref, alt, dataset='gnomad_r4'):
    '''Query gnomAD API for variant frequency

    dataset options: gnomad_r4, gnomad_r3, gnomad_r2_1
    '''
    url = 'https://gnomad.broadinstitute.org/api'

    query = '''
    query ($variantId: String!, $dataset: DatasetId!) {
        variant(variantId: $variantId, dataset: $dataset) {
            exome {
                ac
                an
                af
                homozygote_count
            }
            genome {
                ac
                an
                af
                homozygote_count
            }
        }
    }
    '''

    variant_id = f'{chrom}-{pos}-{ref}-{alt}'
    variables = {'variantId': variant_id, 'dataset': dataset}

    response = requests.post(url, json={'query': query, 'variables': variables})
    return response.json()

Parse gnomAD Response

def parse_gnomad_result(result):
    '''Extract allele frequencies from gnomAD response'''
    data = result.get('data', {}).get('variant', {})
    if not data:
        return None

    exome = data.get('exome', {}) or {}
    genome = data.get('genome', {}) or {}

    return {
        'exome_af': exome.get('af'),
        'exome_ac': exome.get('ac'),
        'exome_an': exome.get('an'),
        'exome_hom': exome.get('homozygote_count'),
        'genome_af': genome.get('af'),
        'genome_ac': genome.get('ac'),
        'genome_an': genome.get('an'),
        'genome_hom': genome.get('homozygote_count')
    }