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clinvar-variation-skill

Query ClinVar Clinical Tables and NCBI Variation APIs for variant summaries and identifier lookups.

5.3k|765|Updated Mar 4, 2026
Search Tags:#VCV#clinvar#api lookup#clinical genomics#ncbi variation#genetic variant#refsnp
One-click install
npx skills add https://github.com/openai/plugins --skill clinvar-variation-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-variation-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/clinvar-variation-skill
Command: npx skills add https://github.com/openai/plugins --skill clinvar-variation-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Researchers and clinicians often need quick, compact summaries of genetic variant records from ClinVar and NCBI Variation without navigating large raw JSON payloads or building API requests by hand.

Core Features & Use Cases

  • Variant Search: Query the ClinVar Clinical Tables endpoint with search terms and receive totals, identifiers, and display rows.
  • Identifier Lookups: Fetch VCV, RCV, SCV, and RefSNP records from the NCBI Variation beta API as compact summaries.
  • Raw Output Saving: Persist full JSON responses to disk with save_raw when complete payloads are needed.
  • Use Case: A genetic counselor asks for the clinical significance of VCV000013080; the Skill returns a trimmed summary instead of a multi-thousand-line JSON document.

Quick Start

Ask the assistant to look up the ClinVar record for VCV000013080 and summarize its clinical significance.

Frequently Asked Questions about clinvar-variation-skill

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

FAQPage Schema
How do I search ClinVar for a genetic variant?▼

Use the search action with a terms field, which calls the ClinVar Clinical Tables API and returns totals, identifiers, and display rows. Start with max_items around 10 to keep results compact.

How do I look up a VCV, RCV, SCV, or RefSNP identifier?▼

Set the action to vcv, rcv, scv, or refsnp and provide the matching identifier field. The script calls the NCBI Variation beta API and returns a compact summary of the record.

Can I get the full raw JSON from the NCBI Variation API?▼

Yes, set save_raw to true and optionally provide raw_output_path. The full response is written to disk and the file path is returned instead of pasting large payloads into chat.

What Python dependencies does the ClinVar lookup script need?▼

The script requires the requests library for HTTP calls to the Clinical Tables and NCBI Variation endpoints. All other imports come from the Python standard library.

Why does the ClinVar output show truncated fields with ellipses?▼

The script compacts nested JSON using max_items and max_depth limits, truncating long strings and arrays to keep summaries readable. Increase max_items or max_depth, or use save_raw, to see more content.

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