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berntpopp
by berntpopp

Get Variant Counts

get_variant_counts
Read-onlyIdempotent

Retrieve residue-level ClinVar variant annotations and Pfam homolog counts for a human transcript, filtered by gnomAD or ClinVar source, with options for single position, range, or whole protein pagination.

Instructions

Return residue-level ClinVar annotations and explicitly-labelled Pfam homolog aggregates on a built landscape, filtered by source (both|gnomad|clinvar). MetaDome has no true residue-level gnomAD count, so it is marked unavailable, never zero. Accepts one position, an inclusive range, or the whole protein (paginated); ClinVar variants include NCBI urls. Signature: get_variant_counts(transcript_id=, position=, position_start=, position_stop=, source=, limit=, offset=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum rows to return (1..1000; default 200).
offsetNoZero-based offset into the result list (for paging).
sourceNoEvidence source to report: both|gnomad|clinvar (default both).both
positionNoA single 1-based residue position.
position_stopNoInclusive stop of a residue range.
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact
transcript_idYesA versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first.
position_startNoInclusive start of a residue range.
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint, so the safety profile is clear. The description adds value by disclosing that MetaDome lacks true residue-level gnomAD counts (marked as unavailable, not zero) and that ClinVar variants include NCBI URLs. This contextual behavior is not captured by 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 concise and well-structured: action first, then key caveat, then scope and output details, ending with signature. Every sentence provides essential information without redundancy. Length is appropriate for the tool's complexity.

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?

Given 8 parameters, 1 required, 100% schema coverage, and no output schema, the description is nearly complete. It covers return type, filtering, positional range handling, pagination, and a notable data limitation. The only gap is a detailed output structure, but the description gives sufficient high-level understanding.

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 baseline is 3. The description adds meaning by explaining the positional parameters (single, range, or whole protein) and mentioning pagination via limit/offset, which clarifies usage beyond the schema. The signature listing reinforces parameter roles but adds minimal new info.

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 residue-level ClinVar annotations and Pfam homolog aggregates on a built landscape, with specific verb 'Return' and resource identification. It distinguishes from siblings by detailing the scope (single position, range, or whole protein) and filtering by source, though sibling differentiation is implicit.

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

Usage Guidelines3/5

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

The description provides implied usage (e.g., for residue-level variant counts) and notes a caveat (gnomAD count unavailable), but lacks explicit guidance on when to use this tool versus alternatives like compare_positions or get_position_tolerance. No exclusions or comparative context is given.

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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