name: 'variant-interpretation-acmg'
description: 'Classifies genetic variants according to ACMG (American College of Medical Genetics) guidelines.'
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
- read_file
- run_shell_command
Variant Interpretation (ACMG)
The Variant Interpretation Skill automates the classification of genetic variants (Pathogenic, Benign, VUS) using a rules-based engine derived from ACMG guidelines.
When to Use This Skill
When analyzing a VCF file for clinical reporting.
To determine the clinical significance of a specific mutation (e.g., BRCA1 c.123A>G).
To aggregate evidence (population freq, computational predictions) into a final verdict.
Core Capabilities
Rule Scoring: Applies codes like PVS1 (Null variant), PM2 (Rare), PP3 (In silico).
Classification: Combines scores to reach a verdict (Pathogenic, Likely Pathogenic, VUS, etc.).
Explanation: Provides the logic/evidence used for the classification.
Workflow
Input: Variant details (Gene, HGVS, Consequence) or Evidence codes directly.
Process: Sums weights of applied ACMG criteria.
Output: Final classification and score breakdown.
Example Usage
User: "Classify a variant with evidence PVS1 and PM2."
1---2name: variant-interpretation-acmg3description: <!--4---5<!--6# COPYRIGHT NOTICE7# This file is part of the "Universal Biomedical Skills" project.8# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>9# All Rights Reserved.10#11# This code is proprietary and confidential.12# Unauthorized copying of this file, via any medium is strictly prohibited.13#14# Provenance: Authenticated by MD BABU MIA1516-->1718---19name: 'variant-interpretation-acmg'20description: 'Classifies genetic variants according to ACMG (American College of Medical Genetics) guidelines.'21measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.22allowed-tools:23 - read_file24 - run_shell_command25---262728# Variant Interpretation (ACMG)2930The **Variant Interpretation Skill** automates the classification of genetic variants (Pathogenic, Benign, VUS) using a rules-based engine derived from ACMG guidelines.3132## When to Use This Skill3334* When analyzing a VCF file for clinical reporting.35* To determine the clinical significance of a specific mutation (e.g., BRCA1 c.123A>G).36* To aggregate evidence (population freq, computational predictions) into a final verdict.3738## Core Capabilities39401. **Rule Scoring**: Applies codes like PVS1 (Null variant), PM2 (Rare), PP3 (In silico).412. **Classification**: Combines scores to reach a verdict (Pathogenic, Likely Pathogenic, VUS, etc.).423. **Explanation**: Provides the logic/evidence used for the classification.4344## Workflow45461. **Input**: Variant details (Gene, HGVS, Consequence) or Evidence codes directly.472. **Process**: Sums weights of applied ACMG criteria.483. **Output**: Final classification and score breakdown.4950## Example Usage5152**User**: "Classify a variant with evidence PVS1 and PM2."5354**Agent Action**:55```bash56python3 Skills/Genomics/Variant_Interpretation/acmg_classifier.py \57 --evidence "PVS1,PM2"58```59606162<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add biotender-max/variant-interpretation-acmg in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
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BioTender-max (@biotender-max) published this skill. Their other Agent Skills are listed on their SkillMD profile.
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