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variants

Read-onlyIdempotent

Retrieve single-variant association results for a trait, genome-wide or within a specific gene, with per-biobank effect direction and cross-biobank replication evidence.

Instructions

Single-variant results for a trait, genome-wide or inside one gene.

Drops below the gene-level burden tests to the individual variants carrying a signal. Without gene this ranks the whole genome for the trait; with gene it restricts to that gene and adds the per-biobank effect-direction tally, the cross-biobank replication evidence.

Still fetched over HTTP rather than shipped in the database: the variant-level format is a separate, actively changing upstream release, an order of magnitude larger than the gene-level table, and rebuilt often enough that a local copy would be stale within the week. Each file is cached permanently once fetched.

Each row links to gnomAD, where population allele frequencies live.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
geneNoRestrict to one gene. Omit for the genome-wide scan.
chromNoRestrict the genome-wide scan to one chromosome ("2", "X").
limitNoMax rows (default 25).
max_pNop-value ceiling. The variant-level threshold is 1.82e-8.
offsetNoSkip this many rows, to page through a long result set.
ancestryNoAll (cross-ancestry meta, default) or a specific stratum. Only meaningful together with `gene`.All
phenotypeYesTrait id or name.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior5/5

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

The description adds rich behavioral context beyond the annotations: explains the HTTP fetch mechanism, reasons for not storing the data locally (large size, frequent upstream rebuilds), caching behavior (permanent caching after first fetch), and links to external data (gnomAD). This goes far beyond the readOnlyHint, openWorldHint, and idempotentHint 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 structured into three clear paragraphs, front-loaded with the core purpose. It contains some explanatory detail (e.g., HTTP fetch rationale) that is valuable but slightly verbose. Overall, each sentence contributes to understanding the tool's behavior and usage.

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 an output schema present, the description need not detail return values. It covers purpose, modes, differentiation from siblings, caching, and external references. It does not explicitly mention pagination or error handling, but the schema descriptions for limit/offset and context signals provide that. The description is largely complete for a read-only data retrieval tool.

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 coverage is 100%, providing baseline 3. The description adds significant value for the 'gene' parameter by explaining it enables additional per-biobank effect-direction and cross-biobank replication evidence. It also reinforces the role of 'max_p' implicitly through mention of the threshold. For other parameters, the schema descriptions suffice.

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 clearly states the tool returns 'single-variant results for a trait, genome-wide or inside one gene', explicitly distinguishing it from gene-level burden tests (likely a sibling tool). It uses a specific verb (returns/fetches) and resource (variants), and explains the two distinct modes of operation.

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 explains when to use genome-wide vs per-gene mode and contrasts with gene-level burden tests. It implies usage context well but does not explicitly state 'when not to use' or name alternative tools. The guidance on caching and HTTP fetch provides operational 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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