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clinvar-database

Query ClinVar variants by gene or position and interpret clinical significance.

94|11|Updated Mar 26, 2026
Search Tags:#genomics#eutilities#variant-interpretation#ftp#clinvar#vcf-annotation
One-click install
npx skills add https://github.com/swaruplab/operon --skill clinvar-database-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/clinvar-database
Command: npx skills add https://github.com/swaruplab/operon --skill clinvar-database-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar data is dispersed across web pages and bulk downloads; this skill enables programmatic access to search, interpret, and integrate ClinVar variant classifications into analyses.

Core Features & Use Cases

  • Programmatic access via E-utilities (esearch, esummary, efetch) to discover variants by gene, disorder, or notation.
  • Bulk data downloads from the ClinVar FTP site to build local databases and pipelines.
  • VCF annotation workflows to enrich variant calls with clinical significance, review status, and cross-references.
  • Use Case: a genomics researcher annotates a patient VCF with ClinVar classifications to prioritize variants for follow-up.

Quick Start

Run a search for BRCA1 pathogenic variants and retrieve their summaries to begin analysis.

Frequently Asked Questions about clinvar-database

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

FAQPage Schema
How do I annotate a VCF file with ClinVar variant significance?▼

You can annotate a VCF with ClinVar variant significance by using this skill to retrieve clinical classifications, review status, and cross-references via E-utilities or FTP downloads, enriching your variant calls for analysis.

What is the best way to programmatically search ClinVar for pathogenic variants by gene?▼

You can programmatically search ClinVar for pathogenic variants by gene using E-utilities endpoints like esearch and esummary to discover variants by gene, disorder, or notation and retrieve their clinical summaries.

Can I build a local ClinVar database from FTP bulk downloads for pipeline integration?▼

Yes, you can build a local ClinVar database for research pipelines by executing bulk data downloads directly from the ClinVar FTP site, consolidating and querying variant significance locally.

How do I retrieve clinical significance and review status for specific genomic positions?▼

You retrieve clinical significance and review status for specific genomic positions by querying ClinVar via E-utilities efetch and esummary endpoints, parsing the results to apply classifications to your variant data.

Does this ClinVar query approach require E-utilities endpoints or can it work with VCF annotation workflows alone?▼

This approach supports both E-utilities endpoints (esearch, esummary, efetch) for programmatic discovery and VCF annotation workflows, allowing you to integrate ClinVar data using either method across research pipelines.

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