Agent skill · research science · aiskillstore
clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
Why this skill is useful
Provides domain-specific knowledge for querying and interpreting ClinVar data that the AI wouldn't reliably generate on its own.
What it needs
About 6k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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: NM000059.3:c.13101313del[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/apireference.md for comprehensive API documentation including: esearch - Search for variants matching criteria esummary - Retrieve variant summaries efetch - Download full XML records elink - Find related records in other NCBI databases Quick example using curl: Best practices: Test queries on the web interface before automating Use API keys to increase rate limits from 3 to 10 requests/second Implement exponential backoff for rate limit errors Set Entrez.email when using Biopython 2. Interpret Clinical Significance Understanding Classifications ClinVar uses standardized terminology for variant classifications. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/clinvar-database