Skip to main content
Glama
smaniches
by smaniches

Generate Precision Medicine Variant Report

generate_variant_clinical_report
Read-onlyIdempotent

Cross-references evidence from eight biomedical databases to produce a single structured variant report with ACMG/AMP criteria mapping and actionability statement for research use.

Instructions

Generate a multi-source variant interpretation report.

Cross-references evidence from up to eight upstream databases for a single HGVS variant into one structured report. The report is a research aid: it surfaces the upstream evidence and the ACMG/AMP criteria that the available evidence supports, but it is not a clinical interpretation and must not be used as a diagnostic without independent review by a qualified clinical laboratory.

  1. Ensembl VEP — functional consequence, SIFT/PolyPhen/CADD predictions

  2. ClinVar — clinical pathogenicity classifications and review status

  3. gnomAD v4 — population allele frequencies across 807,162 individuals

  4. AlphaMissense — deep-learning missense pathogenicity (Cheng et al. 2023)

  5. MONDO — disease ontology context

  6. Open Targets — disease-gene evidence scores

  7. DisGeNET — curated gene-disease association scores

  8. ChEMBL — approved drugs acting on the gene product

The report includes a draft ACMG/AMP criteria checklist with evidence mapping, a structural impact summary, and an actionability statement.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paramsYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

Annotations declare readOnlyHint, idempotentHint, and openWorldHint. The description adds behavioral context beyond annotations, such as the research-aid disclaimer and the fact that it cross-references eight databases. It does not contradict annotations.

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?

The description is well-structured with a clear purpose statement, bullet-pointed list of data sources, and a disclaimer. While somewhat lengthy, each sentence adds value, and critical information is front-loaded.

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

Completeness5/5

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

Given the tool's complexity (single parameter but multiple databases and structured report output), the description thoroughly explains what the report includes and the evidence sources used. The presence of an output schema further supports completeness.

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

Parameters4/5

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

The input schema (shown) has 100% description coverage for all parameters. The description adds meaningful context about the report's content (AMPG criteria, structural impact, actionability) beyond what the schema provides, justifying a score above baseline.

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

Purpose5/5

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

The description clearly states the tool generates a multi-source variant interpretation report for a single HGVS variant, listing specific databases and report components. It distinguishes itself from sibling tools like classify_variant_acmg and triage_variant_3d by focusing on report generation from multiple evidence sources.

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?

The description explicitly notes the report is a research aid, not a clinical interpretation, and requires independent review. It provides clear usage context but does not explicitly exclude scenarios or name alternative tools for specific subtasks.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/smaniches/alphafold-sovereign-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server