clinvar-database

# ClinVar Database ## Overview ClinVar is NCBI's freely accessible archive of reports on relationships between human genetic variants and phenotypes, with supporting evidence. The database aggregates information about genomic variation and its relationship to human health, providing standardized variant classifications used in clinical genetics and research. ## When to Use This Skill This skill should be used when: - Searching for variants by gene, condition, or clinical significance - Interpreting clinical significance classifications (pathogenic, benign, VUS) - Accessing ClinVar data programmatically via E-utilities API - Downloading and processing bulk data from FTP - Understanding review status and star ratings - Resolving conflicting variant interpretations - Annotating variant call sets with clinical significance ## Core Capabilities ### 1. Search and Query ClinVar #### Web Interface Queries Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/ **Common search patterns:** - By gene: `BRCA1[gene]` - By clinical significance: `pathogenic[CLNSIG]` - By condition: `breast cancer[disorder]` - By variant: `NM_000059.3:c.1310_1313del[variant name]` - By chromosome: `13[chr]` - Combined: `BRCA1[gene] AND pathogenic[CLNSIG]` #### Programmatic Access via E-utilities Access ClinVar programmatically using NCBI's E-utilities API. Refer to `references/api_reference.md` for comprehensive API documentation including: - **esearch** - Search for vari...