Gnomad Tools

Configuration File: gnomad_tools.json Tool Type: Local Tools Count: 7

This page contains all tools defined in the gnomad_tools.json configuration file.

Available Tools

gnomad_get_gene (Type: gnomADGraphQLQueryTool)

Get basic gene metadata from gnomAD by gene_symbol or gene_id (Ensembl gene ID). Use `gnomad_…

gnomad_get_gene tool specification

Tool Information:

  • Name: gnomad_get_gene

  • Type: gnomADGraphQLQueryTool

  • Description: Get basic gene metadata from gnomAD by gene_symbol or gene_id (Ensembl gene ID). Use gnomad_search_genes to discover gene_id. Use the returned canonical_transcript_id with gnomad_get_transcript.

Parameters:

  • gene_symbol (string) (optional) Gene symbol (e.g., ‘BRCA1’).

  • gene_id (string) (optional) Ensembl gene ID (e.g., ‘ENSG00000012048’).

  • reference_genome (string) (optional) Reference genome.

Example Usage:

query = {
    "name": "gnomad_get_gene",
    "arguments": {
    }
}
result = tu.run(query)

gnomad_get_gene_constraints (Type: gnomADGetGeneConstraints)

Get gene constraint metrics from gnomAD for a gene symbol (GRCh38). Returns constraint fields und…

gnomad_get_gene_constraints tool specification

Tool Information:

  • Name: gnomad_get_gene_constraints

  • Type: gnomADGetGeneConstraints

  • Description: Get gene constraint metrics from gnomAD for a gene symbol (GRCh38). Returns constraint fields under exac_constraint and gnomad_constraint (e.g., pLI, oe_lof/oe_mis/oe_syn, exp/obs counts).

Parameters:

  • gene_symbol (string) (required) Gene symbol (e.g., ‘BRCA1’, ‘TP53’)

  • reference_genome (string) (optional) Reference genome.

Example Usage:

query = {
    "name": "gnomad_get_gene_constraints",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

gnomad_get_region (Type: gnomADGraphQLQueryTool)

Get basic regional information from gnomAD by genomic interval. Returns genes overlapping the reg…

gnomad_get_region tool specification

Tool Information:

  • Name: gnomad_get_region

  • Type: gnomADGraphQLQueryTool

  • Description: Get basic regional information from gnomAD by genomic interval. Returns genes overlapping the region and a list of variant_id values in the region for the selected dataset. Use those IDs with gnomad_get_variant. Keep regions small to avoid large payloads.

Parameters:

  • chrom (string) (required) Chromosome (e.g., ‘19’).

  • start (integer) (required) 1-based start position.

  • stop (integer) (required) 1-based stop position.

  • reference_genome (string) (optional) Reference genome.

  • dataset (string) (optional) gnomAD dataset ID used for variants(dataset: …). Allowed values: gnomad_r4, gnomad_r4_non_ukb, gnomad_r3, gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2, gnomad_r2_1, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed, exac.

Example Usage:

query = {
    "name": "gnomad_get_region",
    "arguments": {
        "chrom": "example_value",
        "start": 10,
        "stop": 10
    }
}
result = tu.run(query)

gnomad_get_transcript (Type: gnomADGraphQLQueryTool)

Get basic transcript metadata from gnomAD by Ensembl transcript ID (e.g., ENST…). The response …

gnomad_get_transcript tool specification

Tool Information:

  • Name: gnomad_get_transcript

  • Type: gnomADGraphQLQueryTool

  • Description: Get basic transcript metadata from gnomAD by Ensembl transcript ID (e.g., ENST…). The response includes the linked gene object (gene ID + symbol). Use gnomad_get_gene to find a gene’s canonical_transcript_id.

Parameters:

  • transcript_id (string) (required) Ensembl transcript ID (e.g., ‘ENST00000357654’).

  • reference_genome (string) (optional) Reference genome.

Example Usage:

query = {
    "name": "gnomad_get_transcript",
    "arguments": {
        "transcript_id": "example_value"
    }
}
result = tu.run(query)

gnomad_get_variant (Type: gnomADGraphQLQueryTool)

Get basic variant metadata from gnomAD by variant_id (format like ‘19-44908822-C-T’). Use `gnom…

gnomad_get_variant tool specification

Tool Information:

  • Name: gnomad_get_variant

  • Type: gnomADGraphQLQueryTool

  • Description: Get basic variant metadata from gnomAD by variant_id (format like ‘19-44908822-C-T’). Use gnomad_search_variants to discover valid variant_id values from an rsID query. dataset is required by gnomAD and defaults to gnomad_r3.

Parameters:

  • variant_id (string) (required) Variant ID (e.g., ‘19-44908822-C-T’).

  • dataset (string) (optional) gnomAD dataset ID. Allowed values: gnomad_r4, gnomad_r4_non_ukb, gnomad_r3, gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2, gnomad_r2_1, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed, exac.

Example Usage:

query = {
    "name": "gnomad_get_variant",
    "arguments": {
        "variant_id": "example_value"
    }
}
result = tu.run(query)

gnomad_search_genes (Type: gnomADGraphQLQueryTool)

Search for genes in gnomAD by free-text query (typically a gene symbol). Returns matching `ensemb…

gnomad_search_genes tool specification

Tool Information:

  • Name: gnomad_search_genes

  • Type: gnomADGraphQLQueryTool

  • Description: Search for genes in gnomAD by free-text query (typically a gene symbol). Returns matching ensembl_id (Ensembl gene ID) and symbol. Use ensembl_id as gene_id for gnomad_get_gene.

Parameters:

  • query (string) (required) Gene search string (e.g., ‘BRCA1’).

  • reference_genome (string) (optional) Reference genome for the search.

Example Usage:

query = {
    "name": "gnomad_search_genes",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)

gnomad_search_variants (Type: gnomADGraphQLQueryTool)

Search for variants in gnomAD by free-text query (commonly an rsID like ‘rs7412’). Returns matchi…

gnomad_search_variants tool specification

Tool Information:

  • Name: gnomad_search_variants

  • Type: gnomADGraphQLQueryTool

  • Description: Search for variants in gnomAD by free-text query (commonly an rsID like ‘rs7412’). Returns matching variant_id strings. Note: gnomAD’s variant_search response only exposes variant_id. Use the returned variant_id with gnomad_get_variant.

Parameters:

  • query (string) (required) Variant search query (e.g., ‘rs7412’).

  • dataset (string) (optional) gnomAD dataset ID. Allowed values: gnomad_r4, gnomad_r4_non_ukb, gnomad_r3, gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2, gnomad_r2_1, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed, exac.

Example Usage:

query = {
    "name": "gnomad_search_variants",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)