ClinVar Clinical Variants Database

ClinVar Clinical Variants Database

Overview

ClinVar is NCBI's public archive of interpretations of variants submitted by clinical laboratories, researchers, and expert panels. It contains 2M+ variants with clinical significance classifications (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign) for over 6,000 conditions. Access is free and requires no authentication via NCBI E-utilities.

When to Use

• Checking whether a specific variant (rsID, HGVS, or genomic position) has a clinical significance classification
• Retrieving all pathogenic/likely-pathogenic variants in a gene of interest
• Identifying conflicting interpretations between submitting laboratories
• Pulling condition/phenotype associations for a variant (MIM, MeSH, HPO terms)
• Building variant filtering pipelines that prioritize clinically actionable variants
• For somatic cancer variants, also check cosmic-database; for GWAS associations use gwas-database

Prerequisites

• Python packages: requests, xml.etree.ElementTree (stdlib)
• Data requirements: gene symbols, rsIDs, HGVS strings, or ClinVar Variation IDs
• Environment: internet connection; NCBI Entrez email required (set email parameter)
• Rate limits: 3 requests/second unauthenticated; 10/second with API key (free at https://www.ncbi.nlm.nih.gov/account/)

pip install requests
# No additional packages required; xml.etree is part of Python stdlib

Quick Start

import requests

EMAIL = "[email protected]"  # required by NCBI policy

def clinvar_search(query, retmax=10):
    """Search ClinVar and return a list of ClinVar Variation IDs."""
    r = requests.get(
        "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
        params={"db": "clinvar", "term": query, "retmax": retmax,
                "retmode": "json", "email": EMAIL}