db-clinvar

Name: db-clinvar
Availability: InStock
Author: biomaps-infra

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

Updated Mar 13, 2026

Search Tags:#genomics #genetic variants #ncbi #variant interpretation #clinvar #pathogenicity

Ready to run

npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-clinvar

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: db-clinvar
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-clinvar
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-clinvar

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes 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 and interpretation.

Core Features & Use Cases

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

Quick Start

Use the db-clinvar skill to search for pathogenic variants in the BRCA1 gene.

Frequently Asked Questions about db-clinvar

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

FAQPage Schema

How do I retrieve clinical significance for a human genetic variant from ClinVar?▼

To retrieve clinical significance for a human genetic variant from ClinVar, query the database by gene, variant identifier, or clinical assertion using the E-utilities API. This returns the pathogenicity classification and review status for genomic data annotation.

What is the best way to search for pathogenic variants in a specific gene like BRCA1?▼

The best way to search for pathogenic variants in a specific gene like BRCA1 is to query ClinVar using the gene name. The skill retrieves matching clinical significance classifications and supporting evidence for research or clinical interpretation.

Can I use E-utilities API and FTP downloads for bulk ClinVar variant interpretation?▼

Yes, you can use the NCBI E-utilities API for programmatic access and FTP data downloads for bulk analysis to perform ClinVar variant interpretation. This enables genomic data annotation and pathogenicity classification at scale.

Does db-clinvar support searching by clinical assertions and variant identifiers?▼

Yes, db-clinvar supports searching ClinVar by clinical assertions and variant identifiers. This allows researchers and clinicians to quickly access and interpret clinical significance data for human genetic variants.

What are the limitations of using ClinVar for genomic data annotation?▼

A limitation of using ClinVar for genomic data annotation is that pathogenicity classifications depend on submitted clinical assertions and review status. Interpretation requires understanding the supporting evidence behind each variant classification.

Why does my ClinVar variant pathogenicity classification have a conflicting review status?▼

ClinVar variant pathogenicity classifications have conflicting review status when multiple submissions provide differing clinical assertions. The skill retrieves these classifications and review statuses so you can evaluate the supporting evidence.