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Search Genetic Variants

myvariant.variants.search
Read-onlyIdempotent

Search the MyVariant.info database of 450M+ annotated human genetic variants using a flexible query syntax. Query by: dbSNP rsID (e.g. "rs58991260"), gene symbol (e.g. "dbsnp.gene.symbol:BRCA1"), ClinVar clinical significance (e.g. "clinvar.rcv.clinical_significance:Pathogenic"), CADD pathogenicity score (e.g. "cadd.phred:>30"), chromosomal position range (e.g. "chrom:17 AND hg19.start:[41196312 TO 41277500]"), or disease/phenotype keywords (e.g. "clinvar.rcv.conditions.name:breast cancer"). Each hit includes chromosome, genomic position (hg19/hg38), rsID, reference/alternate alleles, CADD PHRED score, ClinVar clinical significance, gnomAD allele frequency, and predicted functional consequences (SnpEff). Data integrates ClinVar, gnomAD, CADD, dbSNP, COSMIC, CIViC, ExAC, and 30+ annotation sources.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
qYesVariant query string. Supports: rsID (e.g. "rs58991260"), gene symbol (e.g. "dbsnp.gene.symbol:BRCA1"), CADD score filter (e.g. "cadd.phred:>20"), ClinVar significance (e.g. "clinvar.rcv.clinical_significance:Pathogenic"), chromosome position (e.g. "chrom:7 AND hg19.start:[140453000 TO 140454000]"), or disease/phenotype keywords (e.g. "clinvar.rcv.conditions.name:breast cancer").
sizeNoMaximum number of variant results to return (1–50, default 10).
fieldsNoComma-separated fields to return per hit. Default: dbsnp,clinvar,cadd,gnomad_exome,gnomad_genome,snpeff,vcf,chrom,hg19. Other useful fields: dbnsfp,cosmic,civic,gwassnps,hg38. Use "all" for every available annotation source.
assemblyNoGenome assembly for coordinate fields in results. "hg19" (GRCh37) or "hg38" (GRCh38). Defaults to hg19.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is clear. The description adds meaningful behavioral context: it searches a massive database, returns specific fields per hit, and integrates 30+ annotation sources. It does not discuss rate limits or result-size caveats, but for a read-only search this is a minor gap. 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.

Conciseness4/5

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

The description is a single dense paragraph, but it is logically ordered: purpose, query examples, return fields, data sources. Every clause adds practical information for using the tool correctly, and there is no fluff. It is on the longer side, but the density of useful examples and context earns its length.

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 complexity, the description is highly complete. It covers purpose, query syntax patterns, output contents, and underlying data sources, while the schema documents all parameters and the output schema documents return values. Nothing an agent needs to call this tool correctly is missing.

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

Parameters4/5

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

Schema description coverage is 100%, so the baseline is 3. The description goes further by providing six distinct query syntax examples for the q parameter that are richer and more varied than the schema description, and it clarifies the fields and assembly parameters through concrete context. This added value justifies a 4.

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 opens with a specific action ('Search the MyVariant.info database...') and clearly identifies the resource and scope (450M+ annotated human genetic variants). It conveys a read/search operation unambiguously. However, it does not explicitly distinguish itself from sibling tools like myvariant.variants.batch or myvariant.variants.info, so it falls short of a 5.

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 extensive, concrete query examples (rsID, gene symbol, ClinVar significance, CADD score, positional range, disease keywords) that effectively tell an agent how to use the tool and for which scenarios. It gives clear context for when this tool is appropriate, but it does not mention exclusions or alternative tools (e.g., using batch for multiple variants), so it lacks explicit when-not-to-use guidance.

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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