bio-clinical-databases-acmg-classification
Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.
npx skills add BioTender-max/awesome-bio-agent-skills --skill acmg-classification --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: requests 2.31+, pandas 2.2+, AutoPVS1 (Xiang 2020), InterVar 2.2+, GeneBe 1.0+ (Stawinski 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 wi
- Version Compatibility
- The Tavtigian Bayesian Point System: The Engine Inside All Modern Classifiers
- PVS1 Decision Tree (Abou Tayoun 2018 Hum Mutat 39:1517)
- Pejaver 2022 PP3/BP4 Calibrated Thresholds (the load-bearing 2024+ calibration)
- PM2Supporting (ClinGen SVI 2020)
- PS3/BS3 Functional Evidence (Brnich 2020 Genome Med 12:3)
- ClinGen SVI Splicing Subgroup 2023 (Walker AJHG 110:1046)
- BS1 / BA1 (Whiffin Max-Credible-AF)
- ClinGen VCEP CSpec Hierarchy
- Cancer Somatic Framework (Li 2017 J Mol Diagn 19:4)
- Decision Tree by Variant Type
- Standard Workflow: ACMG Classification
- Per-Operation Failure Modes
- Reconciliation: When Tools Disagree
What does the bio-clinical-databases-acmg-classification skill do?
Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill acmg-classification --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.