acmg-variant-classifier

name	acmg-variant-classifier
description	ACMG/AMP variant classification skill for systematic pathogenicity assessment
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["variant-analysis","acmg","clinical","pathogenicity"]}
graph	{"domains":["domain:bioinformatics"],"specializations":["specialization:biomedical-informatics"],"skillAreas":["skill-area:statistical-analysis","skill-area:data-analysis","skill-area:python-data-pipelines"],"workflows":["workflow:experiment-design"],"roles":["role:biomedical-engineer","role:research-scientist"]}

ACMG Variant Classifier Skill

Purpose

Enable ACMG/AMP variant classification for systematic pathogenicity assessment following clinical guidelines.

Capabilities

• Automated evidence criteria application
• Population frequency filtering
• In silico prediction integration
• Literature evidence curation
• Inheritance pattern analysis
• Classification report generation

Usage Guidelines

• Apply ACMG criteria systematically
• Document evidence for each criterion
• Consider inheritance patterns in assessment
• Review literature for supporting evidence
• Generate clear classification reports
• Track classification changes over time

Dependencies

• InterVar
• VarSome API
• ClinVar

Process Integration

• Clinical Variant Interpretation (clinical-variant-interpretation)
• Rare Disease Diagnostic Pipeline (rare-disease-diagnostics)
• Newborn Screening Genomics (newborn-screening-genomics)