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Myvariant

by io.github.pipeworx-io
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Variant

variant
Read-onlyIdempotent

Get the full merged annotation for a single human genetic variant by its HGVS id (e.g. "chr7:g.140453136A>T"). COORDINATES ARE hg19/GRCh37 BY DEFAULT — pass assembly "hg38" for GRCh38 positions, which is what gnomAD and Ensembl hand you. Returns annotations aggregated from dbSNP, ClinVar (pathogenicity / clinical significance), CADD and dbNSFP (deleteriousness/conservation scores), and gnomAD (population allele frequencies). Use to look up a known variant and read its pathogenicity and population frequency.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesAn HGVS variant id, e.g. "chr7:g.140453136A>T" (hg19 unless you set assembly).
fieldsNoComma-separated return fields (default: all). e.g. "clinvar,gnomad_genome.af,cadd.phred".
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. Changed3 schema fields changed
    • changedInput schema / examples
      Previous value: -[
-  {
-    "id": "chr7:g.140453136A>T"
-  },
-  {
-    "fields": "clinvar,gnomad_genome.af,cadd.phred",
-    "id": "chr1:g.218631822G>A"
-  }
-]New value: +[
+  {
+    "id": "chr7:g.140453136A>T"
+  },
+  {
+    "fields": "clinvar,gnomad_genome.af,cadd.phred",
+    "id": "chr1:g.218631822G>A"
+  },
+  {
+    "assembly": "hg38",
+    "fields": "dbsnp.rsid,clinvar",
+    "id": "chr1:g.11796321G>A"
+  }
+]
    • 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"
+}
    • changedInput schema / properties / id / description
      Previous value: -"An HGVS variant id, e.g. \"chr7:g.140453136A>T\"."New value: +"An HGVS variant id, e.g. \"chr7:g.140453136A>T\" (hg19 unless you set assembly)."
  2. Changed1 schema field changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "id": "chr7:g.140453136A>T"
+  },
+  {
+    "fields": "clinvar,gnomad_genome.af,cadd.phred",
+    "id": "chr1:g.218631822G>A"
+  }
+]
  3. First observed

TDQS

A4.5/5.0
Behavior5/5

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

The description discloses several behavioral traits beyond what annotations state: the default coordinate system (hg19), the need to pass 'hg38' for GRCh38 positions, and the specific data sources aggregated (dbSNP, ClinVar, CADD, dbNSFP, gnomAD). This adds meaningful context about output content and default behavior, going beyond the readOnly/idempotent hints. There is no contradiction 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 three sentences long, front-loads the core purpose, and includes a highlighted note about coordinates. Every sentence serves a distinct function: stating the operation, clarifying a key default, and summarizing output/use case. There is no redundant or tangential information.

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?

For a relatively simple lookup tool, the description covers the essential information: the input type, the default assembly, the output sources, and the intended use case. The schema covers parameter details, and the description compensates for the lack of an output schema by listing the annotation sources. Nothing critical is missing for an agent to invoke it correctly.

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?

The input schema already describes all three parameters thoroughly (with examples and default values), and schema coverage is 100%. The description adds some context, such as the reason to use hg38 ('what gnomAD and Ensembl hand you'), but it mostly reiterates what the schema already states. Therefore, the description adds limited extra meaning beyond the schema, matching the baseline for high coverage.

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 states a specific verb ('get'), a specific resource ('full merged annotation for a single human genetic variant'), and the method ('by its HGVS id'). It includes a concrete example and clearly distinguishes itself from all sibling tools, none of which deal with genetic variants. The purpose is unambiguous.

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 provides clear context for when to use the tool ('Use to look up a known variant and read its pathogenicity and population frequency') and gives a specific guideline for the assembly parameter (default hg19, pass hg38 for GRCh38 coordinates). It does not explicitly mention when not to use it or name alternatives, but since no sibling tool offers a similar function, this is sufficient.

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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