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tooluniverse-acmg-variant-classification

Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation, VUS resolution, and pathogenicity assessment. Combines ClinVar, gnomAD, computational predictors, and gene-mechanism context.

72

Quality

87%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

The canonical home for this skill is tooluniverse-acmg-variant-classification in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

82%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-structured, highly actionable clinical classification workflow with concrete tool calls, thresholds, and a combination algorithm. It is efficient and clearly sequenced, with only minor conciseness and feedback-loop gaps.

Suggestions

Trim framing prose such as 'The reasoning is:' and the 'LOOK UP, DON'T GUESS' section to tighten conciseness.

Add an explicit validate→fix→re-validate feedback loop in Phase 0 for when variant validation fails.

Consider moving the Tool Parameter Reference table into a references/ file and linking to it from the body to improve progressive disclosure.

DimensionReasoningScore

Conciseness

Mostly efficient and assumes competence, providing specialized thresholds (REVEL >= 0.7, mis_z > 3.09, LOEUF < 0.35) Claude would not reliably know; minor explanatory prose like 'The reasoning is:' and 'LOOK UP, DON'T GUESS' could be trimmed.

4 / 5

Actionability

Fully executable tool calls with exact parameters throughout (e.g. VariantValidator_validate_variant(variant_description=..., genome_build=..., select_transcripts=...)), a complete tool parameter table, and a copy-paste output template covering common cases.

5 / 5

Workflow Clarity

Clear Phase 0–6 sequence with an explicit validation gate ('Validate first') and a combination-rule checklist, but no spelled-out validate→fix→retry feedback loop for failed validation; the task is read-only analysis so the destructive-cap does not apply.

4 / 5

Progressive Disclosure

Well-organized into clearly headed sections with no nested references and content appropriately inline for a decision procedure; the ~244-line monolithic body with no external reference files could potentially split the tool table or criteria detail, preventing a 5.

4 / 5

Total

17

/

20

Passed

Description

92%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, specific description that clearly states both what the skill does and when to use it, with concrete clinical terminology and a distinct niche. Minor room to broaden natural trigger phrasing.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Systematic ACMG/AMP germline variant classification', 'Produces 5-tier verdict ... with cited evidence per criterion', 'VUS resolution, and pathogenicity assessment' — with comprehensive coverage of the domain.

5 / 5

Completeness

Explicitly answers 'what' ('Systematic ACMG/AMP germline variant classification ... Produces 5-tier verdict') and 'when' via the 'Use for variant interpretation, VUS resolution, and pathogenicity assessment' clause.

5 / 5

Trigger Term Quality

Includes natural clinical terms like 'variant interpretation', 'VUS resolution', and 'pathogenicity assessment' that users would say, but is missing some common synonyms/variations a requester might naturally phrase.

4 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (ACMG/AMP germline variant classification) with distinct triggers and named criteria; minimal overlap risk with other skills.

5 / 5

Total

19

/

20

Passed

Validation

100%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

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