What is bio-clinical-databases-acmg-classification?

A genetic-variant classification tool based on the ACMG/AMP framework, a set of evidence rules used to label variants as pathogenic, likely pathogenic, uncertain, likely benign, or benign. It also applies ClinGen specifications and expert-panel rules.

Use it to classify variants, apply evidence criteria such as PVS1 or PP3/BP4, evaluate splicing and functional evidence, and produce a structured clinical interpretation.

It helps organize evidence consistently instead of relying on an unsupported personal judgement. It accounts for gene- and variant-specific guidance and calibrated evidence thresholds.

bio-clinical-databases-acmg-classification — Skill for Claude Code and

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add GPTomics/bioSkills --skill acmg-classification

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/acmg-classification/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/acmg-classification)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/acmg-classification"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/acmg-classification/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/acmg-classification"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/acmg-classification.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 167 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 7,988 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00167	$0.07988
Opus 5	$0.00084	$0.03994
Sonnet 5	$0.00033	$0.01598
Haiku 4.5	$0.00017	$0.00799

Measured 6d ago against content hash 398ed0fd765f, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

bio-clinical-databases-acmg-classification scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/acmg_classify.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

r = requests.get(f'https://api.genebe.net/cloud/api-public/v1/variant',

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-clinical-databases-acmg-classification — 97% identical, 12 lines differ

clinical-databases/acmg-classification/SKILL.md · 468 lines

How it starts

The opening of the file, as written. The whole thing — 468 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: requests 2.31+, pandas 2.2+, AutoPVS1 (Xiang 2020), InterVar 2.2+, GeneBe 1.0+ (Stawiński 2024 Clin Genet). ACMG/AMP Bayesian point system is Tavtigian 2018 Genet Med / 2020 Hum Mutat. Pejaver 2022 AJHG PP3/BP4 calibrated thresholds. ClinGen Splicing Subgroup 2023 (Walker AJHG). v3.2 ACMG SF list (Miller 2023). The ACMG 2.0 framework is in development as of May 2026; not yet published.

Before using code patterns, verify installed versions match. If versions differ:

Python: pip show <package> then help(module.function) to check signatures
CLI: <tool> --version

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. VCEP-specific CSpec rules override default ACMG application; the authoritative directory is https://cspec.genome.network/cspec/ui/svi/all.

ACMG/AMP Variant Classification Framework

'Classify this variant per ACMG/AMP' -> Apply 28-criterion framework using Tavtigian point system; gate on ClinGen SVI specifications and VCEP-specific overrides; assign P / LP / VUS / LB / B classification with evidence trail.

Python (automated): GeneBe API https://api.genebe.net/cloud/api-public/v1/variant
Python (rule-based): InterVar -> python InterVar.py -i input.vcf -b hg38 --table_annovar table_annovar.pl
Web tools: VarSome (commercial), Franklin/Genoox (commercial), ClinGen VCI (gold standard for SVI)
Citation: Richards 2015 Genet Med 17:405 (original framework); Tavtigian 2020 Hum Mutat 41:1734 (point system)

The Tavtigian Bayesian Point System: The Engine Inside All Modern Classifiers

Richards 2015 specified 28 criteria with strength labels (Supporting / Moderate / Strong / Very Strong); combination rules produced P / LP / VUS / LB / B. Tavtigian 2018/2020 demonstrated this framework is mathematically a Bayesian classifier and proposed the naturally-scaled point system that every modern automated classifier implements:

Read the full file on GitHub · 468 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

6d ago First seen · 468 lines · 167 tokens per session scan A 398ed0fd765f

Subscribe to this mod's changes

bio-clinical-databases-acmg-classification is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 25d ago), licensed MIT. It adds 167 tokens to every session and 7,988 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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bio-clinical-databases-acmg-classification