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clinvar-database

Query NCBI ClinVar for clinical significance and pathogenicity classifications of genetic variants.

1|Updated Jan 14, 2026
Search Tags:#genomics#ncbi#variant interpretation#clinvar#pathogenicity#vcf annotation
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill clinvar-database-sologa
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/clinvar-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill clinvar-database-sologa

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, 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 statuses.
  • Data Access: Utilize E-utilities API or download bulk data via FTP.
  • Annotation: Annotate VCF files with clinical significance data.
  • Use Case: A researcher needs to determine if a specific variant in the BRCA1 gene is pathogenic and has been reviewed by an expert panel. They can use this Skill to search ClinVar and retrieve this information.

Quick Start

Use the clinvar-database skill to search for 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 pathogenicity by gene or genomic position?▼

To query ClinVar for variant pathogenicity, search by gene, genomic position, clinical significance, or associated phenotype to retrieve classification and review status data.

What is clinical significance interpretation in ClinVar and how does the review status work?▼

Clinical significance interpretation in ClinVar classifies variant pathogenicity, while review status indicates the assertion credibility based on submitter criteria and expert panel consensus.

Can I annotate a VCF file with clinical significance data from ClinVar?▼

Yes, you can annotate a VCF file with clinical significance data by utilizing NCBI E-utilities API access or downloading bulk ClinVar data for programmatic analysis.

Does the NCBI E-utilities API support bulk data downloads for genomic variant annotation?▼

The NCBI E-utilities API supports programmatic analysis and provides access to bulk ClinVar data downloads via FTP for comprehensive genomic variant annotation.

What are the limitations of using ClinVar for variant interpretation in genomic medicine?▼

ClinVar variant interpretation depends on submitter-provided classifications and review statuses, meaning pathogenicity assertions may vary and lack universal expert panel consensus.

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