variant-interpretation-acmg

name	variant-interpretation-acmg
description	Classifies genetic variants according to ACMG (American College of Medical Genetics) guidelines.

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

1. Rule Scoring: Applies codes like PVS1 (Null variant), PM2 (Rare), PP3 (In silico).
2. Classification: Combines scores to reach a verdict (Pathogenic, Likely Pathogenic, VUS, etc.).
3. Explanation: Provides the logic/evidence used for the classification.

Workflow

1. Input: Variant details (Gene, HGVS, Consequence) or Evidence codes directly.
2. Process: Sums weights of applied ACMG criteria.
3. Output: Final classification and score breakdown.

Example Usage

User: "Classify a variant with evidence PVS1 and PM2."

Agent Action:

python3 Skills/Genomics/Variant_Interpretation/acmg_classifier.py \
    --evidence "PVS1,PM2"