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Variant Analysis

variant_analysis
Read-onlyIdempotent

Classify variants with ACMG guidelines, review population frequencies, ClinVar status, splice impacts, and generate integrated reports.

Instructions

Merged variant-interpretation workflow for ACMG classification, population frequency, ClinVar review, splice review, and full integrated reporting.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
actionYesVariant workflow step.full_report
gene_symbolNoHGNC gene symbol.
variantNoVariant notation, rsID, HGVS, or protein-change string.
inheritanceNoInheritance mode for ACMG scoring.unknown
consequenceNoOptional VEP consequence if already known.
proband_phenotypeNoClinical phenotype context.
populationsNoPopulation IDs to report for gnomAD frequencies.
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false. The description adds context about the workflow steps (ACMG, frequency, ClinVar, splice, reporting) and implies a read-only analysis. No contradictions with 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?

Single sentence that front-loads the key purpose ('Merged variant-interpretation workflow'). Efficient but could slightly expand on key steps without losing conciseness.

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

Completeness3/5

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

Given the tool's complexity (7 parameters, no output schema), the description is adequate for understanding the main purpose but does not explain return values or behavior after execution. Lacks details on output format or next steps.

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

Parameters3/5

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

Schema coverage is 100% with clear parameter descriptions. The description does not add additional meaning beyond the schema, which is acceptable. Baseline score of 3 is appropriate.

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?

Description clearly identifies the tool as a merged variant-interpretation workflow for ACMG classification, population frequency, ClinVar review, splice review, and full reporting. It uses specific verbs and resources, and the scope differentiates it from sibling tools like 'bulk_gene_analysis' or 'pathway_analysis'.

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

Usage Guidelines3/5

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

The description implicitly suggests usage for variant interpretation but does not explicitly state when to use this tool versus alternatives like 'rare_disease_diagnosis' or 'get_gene_info'. No when-to-use or when-not-to-use guidance is provided.

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

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