Genomics MCP

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lookup_variant

Read-only

Retrieves source-attributed evidence for a genomic variant from ClinVar, gnomAD, Ensembl, or Atlas using HGVS, rsID, or VCF input; no clinical verdict.

Instructions

Source-attributed evidence for a variant (ClinVar, gnomAD, Ensembl, optional Atlas). No consensus or clinical verdict. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description
`hgvs`	No
`rsid`	No
`include`	No
`sources`	No	Source names; default all available.
`variant`	No
`assembly`	No

Output Schema

TableJSON Schema

Name	Required	Description	Default
`data`	No
`error`	No	Set when status is error.
`errors`	No	Per-source failures in partial results.
`limits`	No
`status`	Yes
`warnings`	No
`operation`	Yes
`provenance`	No
`truncation`	No
`source_status`	No
`schema_version`	No		1
`metadata_omitted`	No	Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv0.1.1Sep 28, 2026

addedOutput schema / properties / metadata_omitted

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": {
+        "type": "integer"
+      },
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.",
+  "title": "Metadata Omitted"
+}

First observedv0.1.0Sep 24, 2026

TDQS

C2.9/5.0

Behavior3/5

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

Annotations already cover read-only and open-world behavior. The description adds useful context about source attribution and the absence of a clinical verdict, plus optional Atlas as a source. It does not add auth, rate-limit, or return-format details, but the output schema exists.

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 short and front-loaded, quickly stating what evidence is returned and which sources are involved. The final fragment 'Available for: default' is vague filler, but the overall text is efficient.

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

Completeness2/5

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

Given six optional parameters and multiple identifier modes, the description omits critical invocation guidance, such as whether hgvs, rsid, or a variant spec must be supplied. The output schema mitigates return-value concerns, but input completeness is poor.

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 only 17%, so the description must compensate and does not. It never explains accepted variant identifiers (hgvs, rsid, variant spec), include, or assembly; it only indirectly names possible sources, leaving most parameter semantics opaque.

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 clearly states the resource: source-attributed evidence for a variant, with named sources (ClinVar, gnomAD, Ensembl, optional Atlas). It also distinguishes the output from a consensus or clinical verdict. However, it does not explicitly differentiate from siblings such as normalize_variant or get_variants.

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

Usage Guidelines2/5

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

There is no guidance on when to use this tool versus alternatives like normalize_variant, get_variants, or resolve_identifier. The phrase 'Available for: default' is cryptic and provides no actionable usage context or prerequisites.

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