clinvar-database

Query NCBI ClinVar for variant clinical significance and annotate VCF files.

8|Updated Jan 13, 2026

Search Tags:#database #genomics #ncbi #variant interpretation #eutilities #clinvar

Ready to run

npx skills add https://github.com/hxk622/TokenDance --skill clinvar-database-hxk622

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/database/clinvar-database
Command: npx skills add https://github.com/hxk622/TokenDance --skill clinvar-database-hxk622

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps researchers and clinicians quickly access and interpret clinical significance data for genetic variants from the NCBI ClinVar database, streamlining genomic data analysis.

Core Features & Use Cases

Variant Search: Find variants by gene, position, or clinical significance.
Interpretation: Understand pathogenicity classifications and review statuses.
Data Access: Utilize E-utilities API or download bulk data via FTP.
Annotation: Annotate VCF files with ClinVar data.
Use Case: A geneticist needs to determine if a newly identified variant in the BRCA1 gene is pathogenic. They use this Skill to query ClinVar, retrieve its classification, review status, and supporting evidence.

Quick Start

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

Frequently Asked Questions about clinvar-database

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

FAQPage Schema

How do I query ClinVar for variant clinical significance by gene or position?▼

To query ClinVar for variant clinical significance, you can search by gene, genomic position, or clinical significance classification. This skill retrieves pathogenicity data and review statuses directly from the NCBI ClinVar database using the E-utilities API.

Can I annotate a VCF file with ClinVar pathogenicity data?▼

Yes, you can annotate VCF files with ClinVar data. This skill integrates variant clinical significance and pathogenicity classifications from the NCBI ClinVar database directly into your genomic variant call format files for genomic medicine applications.

What is the best way to access bulk ClinVar data for variant interpretation?▼

The best way to access bulk ClinVar data for variant interpretation is via FTP download. This skill supports retrieving large datasets from the NCBI ClinVar database through FTP, alongside programmatic querying using the E-utilities API.

Does this ClinVar database skill retrieve supporting evidence for genetic variants?▼

Yes, this ClinVar database skill retrieves supporting evidence for genetic variants. When querying by gene or position, it accesses the NCBI ClinVar database to return clinical significance, review status, and the underlying supporting evidence.

How do I find all pathogenic variants in a specific gene like BRCA1 from ClinVar?▼

To find all pathogenic variants in a specific gene like BRCA1, you query ClinVar by gene name and filter by clinical significance. This skill retrieves the matching variant classifications and review statuses from the NCBI database.

What are the limitations of using E-utilities to search ClinVar for variant significance?▼

When using E-utilities to search ClinVar for variant significance, limitations include API rate limits and reliance on NCBI database uptime. For large-scale variant interpretation, FTP bulk downloads provide a more robust alternative to programmatic API querying.