Individual skill
clinvar-database
Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.
scientific-skills/Evidence Insight/clinvar-database/SKILL.md
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SKILL.mdcore · 3,424 bytesSKILL.mdcore · 3,424 bytesSKILL.mdcore · 3,424 bytesclinvar-database_audit_result_v1.jsonasset · 12,024 bytesreferences/api_reference.mddoc · 488 bytesreferences/clinical_significance.mddoc · 600 bytesscripts/annotate.pyruns · 1,636 bytesscripts/search.pyruns · 1,263 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
## When to Use
- You need to find ClinVar variant records by **gene**, **condition/phenotype**, or **clinical significance** (e.g., *BRCA1* + *pathogenic*).
- You want to interpret a variant’s **clinical significance** (Pathogenic/Benign/VUS) and **review status** for reporting or triage.
- You need to **annotate a VCF** with ClinVar identifiers and interpretation fields as part of a variant annotation pipeline.
- You want to perform **bulk retrieval** of ClinVar datasets for offline analysis or periodic database refresh.
- You are building a workflow that relies on **NCBI E-utilities** to programmatically query ClinVar.
## Key Features
- **ClinVar search** via NCBI E-utilities using flexible query terms (gene/condition/significance).
- **Clinical interpretation retrieval**, including clinical significance categories and review status.
- **VCF annotation** workflow integration (leveraging `bcftools`) to enrich variants with ClinVar data.