alterlab-clinvar

Query ClinVar variant interpretations and clinical significance via E-utilities and FTP.

58|9|Updated Mar 16, 2026

Search Tags:#api #genomics #data-download #eutilities #variant-interpretation #ftp #clinvar

Ready to run

npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-clinvar

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: alterlab-clinvar
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-clinvar
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-clinvar

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar hosts a large, evolving collection of variant interpretations. Researchers need a reliable way to query, summarize, and integrate these records into pipelines without manual web browsing.

Core Features & Use Cases

Programmatic search, summarize, and retrieval of ClinVar records via E-utilities, FTP, and web services.
Annotate research variant lists with clinical significance, review status, and gene associations across germline, somatic, and related contexts.
Use Case: load large variant lists from sequencing studies to fetch summaries and integrate ClinVar data into analysis workflows.

Quick Start

Query ClinVar for BRCA1 pathogenic variants and fetch summaries to annotate a local variant list.

Frequently Asked Questions about alterlab-clinvar

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

FAQPage Schema

How do I retrieve ClinVar variant interpretations programmatically?▼

To retrieve ClinVar variant interpretations programmatically, you can query the ClinVar E-utilities API or download bulk data via FTP. This allows you to fetch clinical significance and review statuses directly into your research pipelines.

Can I annotate large genomic variant lists with ClinVar clinical significance?▼

Yes, you can annotate large genomic variant lists with ClinVar clinical significance. By loading sequencing study variants, you can fetch summaries and integrate gene associations across germline and somatic contexts into analysis workflows.

What is the best way to access bulk ClinVar data for genomic research?▼

The best way to access bulk ClinVar data for genomic research is through FTP downloads or the E-utilities API. These methods support bulk processing of variant interpretations and integration into annotation pipelines without manual web browsing.

Does this approach support retrieving both germline and somatic variant interpretations?▼

Yes, retrieving ClinVar variant interpretations supports both germline and somatic contexts. You can query records to summarize clinical significance, review status, and gene associations across different variant types for comprehensive annotation.

How do I integrate ClinVar records into a variant annotation pipeline?▼

To integrate ClinVar records into a variant annotation pipeline, query the E-utilities API or use FTP data to fetch clinical significance summaries. This enables automated variant annotation and data processing within genomic research workflows.

When do I need programmatic access to ClinVar data instead of manual web browsing?▼

You need programmatic access to ClinVar data when processing large variant lists from sequencing studies or integrating records into automated pipelines. The E-utilities API and FTP downloads bypass manual web browsing for efficient genomic research workflows.