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Myvariant

by io.github.pipeworx-io
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Query

query
Read-onlyIdempotent

Search aggregated human genetic-variant annotations on MyVariant.info. Accepts an rsID ("rs58991260") or a fielded query ("dbnsfp.genename:CDK2", "clinvar.rcv.clinical_significance:pathogenic"). A bare HGVS id does NOT match here — look one up with the variant tool instead. Each hit merges dbSNP, ClinVar clinical significance, CADD/dbNSFP deleteriousness scores, and gnomAD population allele frequencies. Returns { total, hits, assembly }; hit._id is the HGVS id you can pass to the variant tool, and its coordinates are in the assembly you asked for — hg19 unless you say otherwise.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sizeNoMax hits to return, 1-1000 (default 10).
queryYesrsID, HGVS id, or fielded query. e.g. "rs58991260", "chr1:g.218631822G>A", "dbnsfp.genename:CDK2".
fieldsNoComma-separated return fields (default: all). e.g. "dbsnp,clinvar,cadd.phred,gnomad_genome.af".
assemblyNoGenome build for the coordinates you pass AND the ids you get back: "hg19" (GRCh37, the default) or "hg38" (GRCh38). gnomAD and Ensembl coordinates are GRCh38.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • addedInput schema / properties / assembly
      Added value: +{
+  "description": "Genome build for the coordinates you pass AND the ids you get back: \"hg19\" (GRCh37, the default) or \"hg38\" (GRCh38). gnomAD and Ensembl coordinates are GRCh38.",
+  "type": "string"
+}
  2. Changed1 schema field changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "query": "rs58991260"
+  },
+  {
+    "fields": "dbsnp,clinvar,cadd.phred,gnomad_genome.af",
+    "query": "dbnsfp.genename:CDK2",
+    "size": 20
+  }
+]
  3. First observed

TDQS

A5/5.0
Behavior5/5

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

Annotations already declare readOnly, idempotent, and non-destructive. The description goes beyond by disclosing that each hit merges multiple annotation sources, that returns include total/hits/assembly, and that coordinates follow the requested assembly with a default of hg19. 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.

Conciseness5/5

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

The description is dense but well-organized. It front-loads the core purpose, then gives examples, a critical exclusion, and return structure. Every sentence serves a purpose without redundancy or fluff.

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 moderate complexity (multiple annotation sources, assembly handling, interaction with a sibling tool), the description covers the essential behavioral contract: what inputs are accepted, what outputs look like, how assembly works, and how to use the variant tool for the unsupported case. No significant gaps remain.

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

Parameters5/5

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

The schema already describes all parameters, but the description enriches them: it clarifies that 'assembly' affects both input and output coordinates, gives realistic fielded query examples, and notes that 'query' accepts rsID or fielded queries but not bare HGVS ids. This adds meaning beyond the schema.

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 action (search aggregated human genetic-variant annotations) and clearly distinguishes from the variant tool by explicitly noting that bare HGVS ids are not supported here. Provides concrete query examples, making the tool's purpose unambiguous.

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

Usage Guidelines5/5

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

Explicitly instructs when not to use this tool (bare HGVS id) and directs the user to the variant tool instead, creating clear decision boundaries. Also explains how results can be fed back into the variant tool, giving practical usage context.

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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