clinvar-database

Topics in the source

• ClinVar Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Search and Query ClinVar
• Web Interface Queries
• Programmatic Access via E-utilities
• 2. Interpret Clinical Significance

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. 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 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: NM000059.3:c.13101313del[variant name] By chromosome: 13[chr] Combined: BRCA1[gene] AND pathogenic[CLNSIG] Access ClinVar programmatically using NCBI's E-utilities API. Refer to references/apireference.md for comprehensi

This is an excerpt. Refer to the complete source and its current requirements.