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Draft ACMG/AMP Variant Classification

classify_variant_acmg

Read-onlyIdempotent

Generate a draft ACMG/AMP classification framework from HGVS variant input and inheritance pattern for expert disease-specific evidence review.

Instructions

Generate a draft ACMG/AMP variant classification framework.

Reports computational observations that may inform an expert's later disease-specific ACMG/AMP review. This tool does NOT establish ACMG criteria or assign a pathogenicity class: generic consequence, model scores, and population frequencies are insufficient without clinical disease mechanism, inheritance, and criterion-specific validation.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "params": "<params>"
    },
    "name": "classify_variant_acmg"
  }
}

Input Schema

Name	Required	Description	Default
`params`	Yes

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.5.9Oct 30, 2026

changedInput schema / properties / params / properties / hgvs / description

Previous value: -"HGVS expression for classification, e.g. 'BRCA1:c.181T>G'."New value: +"HGVS expression for unassessed evidence review. Gene-relative terms can find unverified ClinVar candidates; include a versioned RefSeq transcript for exact transcript-text matching."

First observedv1.1.8May 29, 2026

TDQS

A3.7/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, and openWorldHint, so safety and determinism are covered. The description adds genuine context beyond them: the output is an unvalidated computational draft that requires clinical disease mechanism, inheritance, and criterion-specific validation, which materially affects how an agent should present results. It stops short of describing sources consulted or confidence/limitation reporting detail.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short sentences, front-loaded with the action and followed by scope limits and exclusions; no filler. The middle sentence ('Reports computational observations that may inform...') is slightly roundabout but still earns its place by framing the output. Minor tightening would make it a 5.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists and annotations cover safety, so the description's job is mainly to frame intent and limits, which it does thoroughly, including the explicit disclaimer. The one substantive omission is any treatment of the input parameter contract. Otherwise an agent has enough to call this correctly and interpret the result cautiously.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is reported as 0%, so the description needs to compensate for parameter meaning, and it does not mention hgvs or inheritance_pattern at all. Nothing is said about HGVS formatting expectations, transcript versioning, or the default 'Unknown' inheritance value. For a single nested-object parameter with no schema coverage, this is a clear gap.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description gives a concrete verb and resource: 'Generate a draft ACMG/AMP variant classification framework,' and immediately bounds what that output is (computational observations, not a classification). That is much more specific than a restatement of the title. It does not explicitly distinguish itself from near neighbors such as generate_variant_clinical_report or triage_variant_3d, so it stops short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Strong negative guidance: the tool does not establish criteria or assign a pathogenicity class, and is positioned as input to an expert's later disease-specific review. That effectively tells an agent when this is appropriate (preliminary evidence gathering) and when it is not (authoritative classification). It never names an alternative tool to use instead, which keeps it out of 5 territory.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.