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.
npx skills add LeonChaoX/qinyan-academic-skills --skill clinvar-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 chr
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Search and Query ClinVar
- 2. Interpret Clinical Significance
- 3. Download Bulk Data from FTP
- 4. Process and Analyze ClinVar Data
- 5. Handle Conflicting Interpretations
- 6. Track Classification Updates
- 7. Submit Data to ClinVar
- Workflow Examples
- Example 1: Identify High-Confidence Pathogenic Variants in a Gene
- Example 2: Annotate VCF with ClinVar Classifications
- Example 3: Analyze Variants for a Specific Disease
Search for pathogenic BRCA1 variants curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json" Download latest monthly XML release wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz Download VCF for GRCh38 wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz Filter pathogenic variants bcftools view -i 'INFO/CLNSIG~"Pathogenic"' clinvar.vcf.gz Extract specific genes bcftools view -i 'INFO/GENEINFO~"BRCA"' clinvar.vcf.gz
What does the clinvar-database skill do?
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.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill clinvar-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.