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tooluniverse-variant-interpretation

Clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogenicity assessment with cited criteria, structure-based variant impact (AlphaFold/PDB), non-coding/regulatory variant effect prediction with sequence deep-learning models (AlphaGenome, Enformer, Borzoi, ChromBPNet, Evo 2), and producing clinical-grade variant reports for return of results or molecular tumor boards. Use this whenever a user asks about a variant's significance, an intronic/promoter/enhancer/UTR non-coding variant's functional impact, or needs ACMG classification — even if they don't say "ACMG".

72

Quality

88%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

77%

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

The body is a thorough, actionable clinical workflow with an executable classifier and clear phased checkpoints, but it carries some unnecessary explanatory prose and signals five reference files that are absent from the bundle.

Suggestions

Provide the referenced bundle files (ACMG_CLASSIFICATION.md, CODE_PATTERNS.md, CHECKLIST.md, EXAMPLES.md, TOOLS_REFERENCE.md) or inline their critical content, since the body depends on them for thresholds, patterns, and verification.

Tighten the narrative sections on conflicting evidence and epidemiology-vs-functional data into terse rules, removing framing prose Claude already knows.

Verify the cross-skill path in 'Cross-Skill References' (skills/tooluniverse-sequence-analysis/scripts/amino_acids.py) resolves, or make the dependency explicit in prerequisites.

DimensionReasoningScore

Conciseness

Mostly dense and actionable, but includes explanatory prose Claude already knows (e.g. "This is one of the most challenging scenarios in variant interpretation" and the narrative on epidemiological vs functional evidence) that could be trimmed.

2 / 3

Actionability

Provides concrete tools with parameters and return shapes, an executable Python ACMG classifier, gene-specific frequency thresholds, and explicit tool-failure fallback chains — copy-paste ready.

3 / 3

Workflow Clarity

Clear phased sequence with an explicit short-circuit checkpoint (Phase 2.9 expert-panel check), conflict-handling rules, and validation-style fallback loops for risky classification decisions.

3 / 3

Progressive Disclosure

References five bundle files (ACMG_CLASSIFICATION.md, CODE_PATTERNS.md, CHECKLIST.md, EXAMPLES.md, TOOLS_REFERENCE.md) inline and well-signaled, but none of these files exist in the skill directory, so the disclosed structure is not actually present.

2 / 3

Total

10

/

12

Passed

Description

100%

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

The description is specific, action-oriented, and in third person, with concrete capabilities and an explicit trigger clause covering both coding and non-coding variant scenarios. Trigger terms mirror natural user language well, and the niche is clearly distinct.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — "VUS classification", "pathogenicity assessment with cited criteria", "structure-based variant impact (AlphaFold/PDB)", "non-coding/regulatory variant effect prediction", "clinical-grade variant reports" — in third person.

3 / 3

Completeness

Explicitly answers both what it does ("Clinical variant interpretation from raw variant calls to ACMG-classified recommendations...") and when to use it ("Use this whenever a user asks about a variant's significance...").

3 / 3

Trigger Term Quality

Strong coverage of natural user phrasings such as "variant's significance", "non-coding variant", "intronic/promoter/enhancer/UTR", and "ACMG classification" that a clinician or researcher would actually say.

3 / 3

Distinctiveness Conflict Risk

Occupies a clearly distinct clinical-variant niche with specific triggers (ACMG classification, non-coding variant effect, molecular tumor boards) unlikely to overlap with generic analysis skills.

3 / 3

Total

12

/

12

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

Table of Contents

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