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🦖 CNV ACMG Classifier · clawbio | DecimalAI

scienceby clawbio

🦖 CNV ACMG Classifier

clawbio/cnv-acmg-classifier

Source clawbio/clawbio ↗License MIT

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.

SkillScore86Maintained

Automatic

Clinical / Healthcare pack

Last verified 8/16/2026

What it changes

Passed 16 of 19 test cases with the skill, and 6 of 19 without it.

Without skill32%

With skill86%

Checks it passed that the model alone missed

Custom dosage map path is passed using the --dosage-map argument flag.
Custom gene model path is passed using the --gene-model argument flag.
Partial 5' deletion affecting 5'UTR alone scores 0.00 under category 2C-2.

and 14 more in the full report

12 fixed7 passed either way3 still failing0 broke

Pass-rate lift: +55 pp
Tokens: +155%
Agent turns: 0%
Response time: -46%

Model gemini-3.6-flashMeasured 8/16/2026v119 of 22 cases passed with skill · 19 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/clawbio-cnv-acmg-classifier/SKILL.md https://app.decimal.ai/s/clawbio-cnv-acmg-classifier/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add clawbio-cnv-acmg-classifier, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/clawbio-cnv-acmg-classifier/ and pins it in .decimal/skills.lock

decimalai skills add clawbio-cnv-acmg-classifier

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/clawbio-cnv-acmg-classifier/SKILL.md https://app.decimal.ai/s/clawbio-cnv-acmg-classifier/SKILL.md

Raw file: /s/clawbio-cnv-acmg-classifier/SKILL.md ↗ · machine-readable summary at /s/clawbio-cnv-acmg-classifier.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 12 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 12

Prompt

A 50 kb deletion falls entirely within a region documented in ClinGen as benign with no functional dosage sensitivity. What points are assigned in Section 2? Provide the category code and points.

What was checked, without and with the skill
Checked	Without skill	With skill
Complete containment within an established benign region scores -1.00 under section 2F.	Missed	Passed

case-18 · gemini-3.6-flash · 8/16/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md198 linessingle file

🦖 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

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

Scope

One skill, one task. This skill classifies germline CNV/SV dosage effects and nothing else. It does not call variants, annotate SNVs, or predict phenotypes.

Input Formats

Track record

Benchmark

16 / 19

test cases passed, vs 6 / 19 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

clawbio / clawbio

skills/cnv-acmg-classifier/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

mims-harvard/tooluniverse-structural-variant-analysisStructural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted criteria with ClinGen HI/TS dosage scores, gnomAD frequencies, and ClinVar evidence. Produces 5-tier classification with explicit per-criterion evidence. Use for clinical genomics SV review, dosage-sensitivity assessment, breakpoint analysis, and CNV pathogenicity calls. Gene-dosage-driven reasoning.Close match-5 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

🦖 CNV ACMG Classifier

Trigger

Why This Exists

Core Capabilities

Scope

Input Formats

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills