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clinvar-database

Query NCBI ClinVar for genetic variant clinical significance classifications.

1|1|Updated Mar 13, 2026
Search Tags:#genetics#ncbi#variant interpretation#clinvar#pathogenicity#genomic medicine
One-click install
npx skills add https://github.com/youyinnn/skills-collection --skill clinvar-database-youyinnn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/youyinnn/skills-collection/tree/main/plugins/data-preparation-and-processing/skills/clinvar-database
Command: npx skills add https://github.com/youyinnn/skills-collection --skill clinvar-database-youyinnn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill simplifies the process of accessing and interpreting clinical significance data for genetic variants from the NCBI ClinVar database, crucial for genomic medicine research.

Core Features & Use Cases

  • Variant Search: Query ClinVar by gene, position, or clinical significance.
  • Interpretation: Understand pathogenicity classifications and review status.
  • Data Download: Access bulk data via FTP for large-scale analysis.
  • Use Case: A researcher needs to find all pathogenic variants in the BRCA1 gene with a high review status to identify high-confidence disease-associated mutations for a study.

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 the clinical significance of genetic variants?▼

Query ClinVar by searching with gene symbols, genomic positions, or condition names to retrieve clinical significance classifications. You can filter results specifically for pathogenic, benign, or VUS variants.

How do I find high-confidence pathogenic variants in a specific gene like BRCA1?▼

Find high-confidence pathogenic variants by querying ClinVar for a specific gene and filtering by review status. This isolates high-confidence disease-associated mutations for genomic medicine studies.

Can I download bulk ClinVar data via FTP for large-scale genomic analysis?▼

Yes, you can access and download bulk ClinVar data via FTP for large-scale analysis. This allows researchers to process comprehensive variant significance datasets offline.

What do pathogenic, benign, and VUS classifications mean in ClinVar variant interpretation?▼

Pathogenic, benign, and VUS are clinical significance classifications in ClinVar variant interpretation. Pathogenic indicates disease-causing, benign indicates harmless, and VUS signifies uncertain significance.

Does the ClinVar database skill support searching via the NCBI E-utilities API?▼

Yes, ClinVar data access supports using the NCBI E-utilities API. This enables automated querying and retrieval of clinical significance data for genomic medicine applications.

What is the best way to interpret ClinVar review status when assessing variant pathogenicity?▼

Interpret ClinVar review status by checking the confidence level assigned to the clinical significance assertion. Higher review status indicates multiple independent submissions supporting the pathogenicity classification.

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