clinvar-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/) ```bash pip install requests # No additional packages required; xml.etree is part of Python stdlib ``` ## Quick Start ```python import requests EMAIL ...