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clinvar-database

Query NCBI ClinVar for clinical significance of genetic variants.

Updated Mar 10, 2026
Search Tags:#genomics#ncbi#variant interpretation#clinvar#pathogenicity#genetic variation
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill clinvar-database-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/clinvar-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill clinvar-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides access to the NCBI ClinVar database, enabling users to quickly find and interpret the clinical significance of genetic variants, which is crucial for genomic medicine and research.

Core Features & Use Cases

  • Variant Search: Query ClinVar by gene, position, clinical significance, or condition.
  • Interpretation: Understand pathogenicity classifications and review status.
  • Data Access: Utilize E-utilities API or download bulk data via FTP.
  • Annotation: Annotate variant call files (VCFs) with ClinVar data.
  • Use Case: A researcher needs to determine if a specific variant found in a patient's exome sequencing data is known to be pathogenic for a particular disease. This Skill can be used to search ClinVar for that variant and retrieve its associated clinical significance and supporting evidence.

Quick Start

Use the clinvar-database skill to find pathogenic variants for the gene BRCA1.

Frequently Asked Questions about clinvar-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find the clinical significance of a genetic variant in ClinVar?▼

To find the clinical significance of a genetic variant in ClinVar, query the NCBI database by gene, genomic position, or phenotype. This retrieves pathogenicity classifications and supporting evidence for genomic medicine workflows.

Can I search ClinVar for pathogenic variants associated with a specific gene like BRCA1?▼

Yes, you can search ClinVar for pathogenic variants associated with a specific gene like BRCA1. The skill supports querying by gene name to retrieve variant clinical significance and associated disease conditions.

What is the best way to annotate a VCF file with ClinVar pathogenicity data?▼

The best way to annotate a VCF file with ClinVar pathogenicity data is by querying the database via E-utilities API or FTP bulk downloads. This allows you to map variant positions to their clinical significance classifications.

Does this skill support accessing ClinVar through the E-utilities API and FTP bulk downloads?▼

Yes, this skill supports accessing ClinVar data through both the E-utilities API for targeted queries and FTP bulk downloads for large-scale data retrieval. This facilitates diverse genomic medicine and research workflows.

How do I interpret ClinVar review status and pathogenicity classifications for exome sequencing data?▼

To interpret ClinVar review status and pathogenicity classifications for exome sequencing data, query the variant to retrieve its clinical significance and supporting evidence. This helps determine if a variant is known to be pathogenic for a particular disease.

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