get_variant
Retrieve detailed genetic variant information from gnomAD databases to analyze population frequencies, constraint scores, and genomic data for research and clinical applications.
Instructions
Get detailed information about a specific variant
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| variant_id | Yes | Variant ID in format: chr-pos-ref-alt (e.g., 1-55516888-G-A) | |
| dataset | No | Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc.) | gnomad_r4 |
Implementation Reference
- src/index.ts:668-674 (handler)The core handler logic for the 'get_variant' tool within the CallToolRequestSchema handler. It invokes the GraphQL query using makeGraphQLRequest with the provided variant_id and parsed dataset_id.
case "get_variant": result = await makeGraphQLRequest(QUERIES.getVariant, { variantId: args.variant_id as string, datasetId: parseDatasetId((args.dataset as string) || "gnomad_r4"), }); formattedResult = result.data?.variant || null; break; - src/index.ts:461-479 (schema)Input schema definition and registration for the 'get_variant' tool in the ListTools response.
{ name: "get_variant", description: "Get detailed information about a specific variant", inputSchema: { type: "object", properties: { variant_id: { type: "string", description: "Variant ID in format: chr-pos-ref-alt (e.g., 1-55516888-G-A)", }, dataset: { type: "string", description: "Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc.)", default: "gnomad_r4", }, }, required: ["variant_id"], }, }, - src/index.ts:117-186 (schema)GraphQL query schema (QUERIES.getVariant) that defines the structure and fields retrieved for the variant data.
getVariant: ` query GetVariant($variantId: String!, $datasetId: DatasetId!) { variant(variantId: $variantId, dataset: $datasetId) { variant_id reference_genome chrom pos ref alt rsids caid colocated_variants multi_nucleotide_variants { combined_variant_id changes_amino_acids n_individuals other_constituent_snvs } exome { ac an ac_hemi ac_hom faf95 { popmax popmax_population } filters populations { id ac an ac_hemi ac_hom } } genome { ac an ac_hemi ac_hom faf95 { popmax popmax_population } filters populations { id ac an ac_hemi ac_hom } } transcript_consequences { gene_id gene_symbol transcript_id consequence_terms is_canonical major_consequence polyphen_prediction sift_prediction lof lof_filter lof_flags } } } `, - src/index.ts:44-61 (helper)Helper function makeGraphQLRequest used by the get_variant handler to execute the GraphQL query against the gnomAD API.
async function makeGraphQLRequest(query: string, variables: Record<string, any> = {}): Promise<GnomadResponse> { const response: Response = await fetch(GNOMAD_API_URL, { method: "POST", headers: { "Content-Type": "application/json", }, body: JSON.stringify({ query, variables, }), }); if (!response.ok) { throw new Error(`HTTP error! status: ${response.status}`); } return await response.json() as GnomadResponse; } - src/index.ts:384-400 (helper)Helper function parseDatasetId used to validate and default the dataset parameter in the get_variant handler.
function parseDatasetId(dataset: string): string { const validDatasets = [ "gnomad_r2_1", "gnomad_r3", "gnomad_r4", "gnomad_sv_r2_1", "gnomad_sv_r4", "gnomad_cnv_r4", "exac", ]; const datasetLower = dataset.toLowerCase(); if (!validDatasets.includes(datasetLower)) { return "gnomad_r4"; // Default to latest version } return datasetLower; }