bio-clinical-databases-clinvar-lookup

Version Compatibility

Reference examples tested with: Entrez Direct 21.0+, bcftools 1.19+

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

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

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

ClinVar Lookup

REST API Queries

Goal: Retrieve ClinVar pathogenicity classifications and disease associations for variants via REST API.

Approach: Query NCBI E-utilities endpoints with variant IDs, gene symbols, or HGVS notation and parse JSON responses.

"Look up this variant in ClinVar" → Query ClinVar database for clinical significance, review status, and disease associations.

• Python: requests.get() against NCBI E-utilities (requests)
• CLI: esearch/efetch (Entrez Direct)

Query by Variant ID

import requests

def query_clinvar_by_id(variation_id):
    '''Query ClinVar by variation ID'''
    url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi'
    params = {
        'db': 'clinvar',
        'id': variation_id,
        'retmode': 'json'
    }
    response = requests.get(url, params=params)
    return response.json()

result = query_clinvar_by_id('16609')

Search by Gene

def search_clinvar_gene(gene_symbol, pathogenic_only=False):
    '''Search ClinVar for variants in a gene'''
    url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'

    term = f'{gene_symbol}[gene]'
    if pathogenic_only:
        term += ' AND pathogenic[clinical_significance]'

    params = {
        'db': 'clinvar',
        'term': term,
        'retmax': 500,
        'retmode': 'json'
    }
    response = requests.get(url, params=params)
    return response.json()

Search by HGVS

def search_clinvar_hgvs(hgvs):
    '''Search ClinVar by HGVS notation'''
    url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
    params = {
        'db': 'clinvar',
        'term': f'{hgvs}[variant name]',
        'retmode': 'json'
    }
    response = requests.get(url, params=params)
    return response.json()