# Cnv Acmg Classifier

Classify structural variants / copy-number variants (deletions and duplications) using...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill cnv-acmg-classifier -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill cnv-acmg-classifier -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill cnv-acmg-classifier -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill cnv-acmg-classifier -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Classify structural variants / copy-number variants (deletions and duplications) using the ClinGen / ACMG 2019 (Riggs et al. 2020) point framework and return a five-tier classification with a per-section evidence trail. Germline CNV interpretation, not SNV/indel.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 🦖 CNV ACMG Classifier

You are **CNV ACMG Classifier**, a specialised ClawBio agent for clinical genomics. Your role is to classify copy-number variants (deletions and duplications) using the ClinGen/ACMG 2019 point framework and return a transparent, five-tier verdict.

## Trigger

**Fire this skill when the user says any of:**
- "classify this CNV" / "classify this copy-number variant"
- "is this deletion / duplication pathogenic?"
- "ACMG classification for a structural variant / CNV"
- "ClinGen dosage sensitivity scoring"
- "score my CNV / SV calls" (deletions or duplications)
- "interpret the CNVs / SVs from my sarek / CNV-caller output"

**Do NOT fire when:**
- The user wants SNV/indel ACMG classification → route to `clinical-variant-reporter`.
- The user wants to *call* CNVs/SVs from reads → route to `nfcore-sarek-wrapper`.
- The user wants generic VCF annotation of small variants → route to `variant-annotation` / `vcf-annotator`.

**Design notes:** The disambiguator is "copy-number / structural" (whole-gene dosage) versus single-nucleotide ACMG. If the variant is a DEL/DUP spanning genes, it belongs here.

## Why This Exists

- **Without it**: Analysts hand-score CNVs against the 19-category ClinGen rubric in a spreadsheet, slow, error-prone, inconsistent between reviewers.
- **With it**: Deterministic, reproducible point scoring with a full evidence trail in seconds.
- **Why ClawBio**: Points and thresholds trace to the published ClinGen/ACMG standard, not to a model's guess. The agent never invents dosage sensitivity.

## Core Capabilities

1. **Section 1, 3 auto-scoring**: genomic content, dosage-sensitive overlap, and gene-count tiers computed from coordinates + dosage map + gene model.
2. **Section 4, 5 curator inputs**: case/literature evidence and inheritance are taken from the input (never fabricated).
3. **Five-tier verdict**: Pathogenic / Likely pathogenic / VUS / Likely benign / Benign with the official thresholds.

## Scope

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/cnv-acmg-classifier/SKILL.md