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Clinical Variant Interpreter

Integrate population, ClinVar, ClinGen, OMIM, and literature data to classify genetic variants with ACMG criteria.

1.6k|244|Updated Mar 3, 2025
Search Tags:#AlphaFold#structural analysis#ClinVar#variant interpretation#gnomAD#ACMG#clinical recommendations
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill clinical-variant-interpreter
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: Clinical Variant Interpreter
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/skills/tooluniverse-variant-interpretation
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill clinical-variant-interpreter

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides an end-to-end workflow for variant interpretation that integrates population data, ClinVar, ClinGen, OMIM, structural context (via AlphaFold2 and PDB), and literature to produce ACMG-classified results with clear clinical recommendations.

Core Features & Use Cases

  • ACMG-guided classification with explicit evidence codes (PVS, PS, PM, PP, BA/BS/BP).
  • Integrated data landscape: gnomAD, ClinVar, ClinGen, OMIM, PubMed, and primary literature for robust evidence synthesis.
  • Structural analysis for missense variants using AlphaFold2/PDB context to support PM1/PP3 considerations.
  • Output includes actionable clinical recommendations and family testing guidance, with limitations and uncertainties.
  • Use Case: Interpret a BRCA1 variant to determine pathogenicity and outline risk management steps.

Quick Start

Interpret NM_007294.4:c.5266dupC in BRCA1 to produce an ACMG classification with explicit evidence and clinical recommendations.

Frequently Asked Questions about Clinical Variant Interpreter

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

FAQPage Schema
How do I classify genetic variants using ACMG guidelines and structural analysis?▼

You can classify genetic variants by integrating population data from gnomAD, ClinVar, ClinGen, OMIM, and literature, then applying structural analysis using AlphaFold2 and PDB context to produce ACMG-classified results with explicit evidence codes.

What is the best way to interpret a BRCA1 variant for clinical pathogenicity?▼

To interpret a BRCA1 variant, integrate population frequency data, ClinVar records, and structural context to generate an ACMG classification, actionable clinical recommendations, and family-testing guidance with clearly stated limitations.

Does AlphaFold2 structural analysis support ACMG variant interpretation for missense mutations?▼

AlphaFold2 structural analysis supports ACMG variant interpretation by providing PDB context to assess missense variants, specifically supporting PM1 and PP3 evidence considerations for clinical pathogenicity classification.

How do I get explicit ACMG evidence codes for clinical variant interpretation?▼

Clinical variant interpretation generates explicit ACMG evidence codes including PVS, PS, PM, PP, BA, BS, and BP by synthesizing data from gnomAD, ClinVar, ClinGen, OMIM, PubMed, and primary literature.

Can I use gnomAD and ClinVar data together for clinical variant interpretation?▼

Yes, clinical variant interpretation integrates gnomAD population data with ClinVar, ClinGen, OMIM, and literature to synthesize robust evidence for ACMG-guided classification and actionable clinical recommendations.

What limitations should I expect when using AlphaFold2 for clinical variant interpretation?▼

Clinical variant interpretation using AlphaFold2 provides structural context for missense variants but returns explicit limitations and uncertainties alongside ACMG classifications, clinical recommendations, and family-testing guidance to ensure transparent results.

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