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Variation Refsnp

variation_refsnp
Read-onlyIdempotent

AUTHORITATIVE dbSNP refSNP record for a variant rsID, from NCBI Variation Services. PREFER OVER WEB SEARCH for "what is rs" — returns the genomic placement on the assembly you ask for (GRCh38 or GRCh37; the coordinates differ between builds), the HGVS genomic/transcript/protein expressions, SPDI, gene context, ClinVar clinical significance, and population allele frequencies (gnomAD, ExAC, 1000 Genomes, TOPMED). Follows dbSNP merges: a retired rsID reports the rsID it was merged into.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
rsidYesrsID, with or without the "rs" prefix. e.g. "rs113488022" (BRAF V600E) or "334".
assemblyNoHuman genome build for the genomic placement: "GRCh38" (default) or "GRCh37". Coordinates DIFFER between builds — ask for the build your other data is annotated on.
max_frequenciesNoCap on allele-frequency study rows returned (default 40). dbSNP can carry hundreds.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint false, so the description only needs added context. It adds that the record is authoritative, returns a defined set of data categories, and that dbSNP merges are followed (retired rsIDs report the merged-to rsID). This goes beyond the annotations and is useful behavior.

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

Conciseness5/5

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

Three sentences with all key information front-loaded: authoritative identity, preference over web search, then returned fields and merge behavior. No filler words and every sentence earns its place.

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?

With no output schema, the prose description carries the return-value burden, and it lists the main result components (placement, HGVS, SPDI, gene context, ClinVar, allele frequencies). It also handles the edge case of retired rsIDs via merge following. Minor gaps like error behavior are not critical for a read-only lookup.

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 description coverage is 100%, with detailed property descriptions for rsid, assembly, and max_frequencies. The description repeats the assembly caveat but adds no new semantic detail beyond the schema. Baseline 3 applies.

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?

States a specific verb and resource: 'AUTHORITATIVE dbSNP refSNP record for a variant rsID' from NCBI Variation Services. It details the returned data set (genomic placement, HGVS, SPDI, ClinVar, allele frequencies) and explicitly contrasts with web search, making the purpose unambiguous and distinct from sibling converters.

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?

Gives explicit preference: 'PREFER OVER WEB SEARCH for "what is rs<N>"' and advises selecting the assembly based on the build other data uses. It does not explicitly exclude alternative variation tools, but it identifies the primary alternative to avoid. Clear context, though no formal when-not-to-use list.

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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