clinvar-database

Query NCBI ClinVar for clinical significance of human genetic variants.

557|98|Updated Nov 7, 2025

Search Tags:#genetics #ncbi #variant interpretation #clinvar #pathogenicity #genomic medicine

Ready to run

npx skills add https://github.com/jimmc414/Kosmos --skill clinvar-database-jimmc414

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/clinvar-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill clinvar-database-jimmc414

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 query and interpret the clinical significance of human genetic variants, crucial for genomic medicine and research.

Core Features & Use Cases

Variant Interpretation: Understand pathogenicity classifications (Pathogenic, Benign, VUS) and review statuses.
Data Access: Query ClinVar via E-utilities API or download bulk data from FTP.
Annotation: Annotate variant call sets (VCFs) with clinical significance.
Use Case: A researcher needs to determine if a specific variant in the BRCA1 gene is associated with an increased risk of breast cancer. They can use this Skill to query ClinVar, retrieve the variant's classification, and understand the supporting evidence.

Quick Start

Use the clinvar-database skill to find all pathogenic variants for 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 a specific genetic variant?▼

To query ClinVar for clinical significance, you can use the NCBI E-utilities API for programmatic access or download bulk data from FTP. This retrieves pathogenicity classifications like Pathogenic, Benign, or VUS for human genetic variants.

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

Yes, you can annotate VCF files with clinical significance from ClinVar. This process adds pathogenicity classifications and review statuses to your variant call sets, which is crucial for genomic medicine applications and research analysis.

What is the difference between Pathogenic, Benign, and VUS in ClinVar variant interpretation?▼

In ClinVar variant interpretation, Pathogenic and Benign classifications indicate disease-causing or harmless variants respectively, while VUS (Variant of Uncertain Significance) lacks sufficient evidence. These classifications support genomic medicine decisions and research.

Do I need to understand XML and VCF data formats to use the ClinVar database?▼

Yes, understanding XML and VCF data formats is required to use the ClinVar database effectively. Programmatic access via E-utilities API and variant call set annotation require parsing these formats to retrieve and interpret clinical significance.

What's the best way to find all pathogenic variants for the BRCA1 gene in ClinVar?▼

The best way to find pathogenic variants for the BRCA1 gene is querying ClinVar via the NCBI E-utilities API. This retrieves variant classifications and supporting evidence, enabling you to identify associations like breast cancer risk.

When should I download bulk data from the ClinVar FTP instead of using the E-utilities API?▼

You should download bulk data from the ClinVar FTP instead of using the E-utilities API when you need to perform large-scale variant interpretation or annotate entire VCF files locally, rather than querying individual variants on demand.