Gnomad Tools#

Configuration File: gnomad_tools.json Tool Type: Local Tools Count: 11

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. The returned chrom/start/stop are in the assembly named by reference_genome, which gnomAD reports itself on both the gene object and the top level of the response (GRCh38 unless the reference_genome argument says otherwise). Coordinates are not comparable across assemblies: BRCA2 is 13:32,315,086-32,400,268 on GRCh38 and 13:32,889,611-32,973,805 on GRCh37.

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). Note: does NOT include LOEUF, missense Z-score, or synonymous Z-score – for the full constraint panel (pLI + LOEUF + mis_z + syn_z), use gnomad_get_constraint instead.

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. dataset defaults to gnomad_r3 (GRCh38, genomes only), so the variant list is the one that callset contains. Defaults deliberately differ across this gnomAD family: gnomad_get_variant, gnomad_search_variants and gnomad_get_region default to gnomad_r3 while gnomad_get_variant_populations and gnomad_get_constraint default to gnomad_r4, so gnomad_get_variant and gnomad_get_variant_populations report different numbers for the same variant unless you pass the same dataset to both. Every response echoes dataset and reference_genome (gnomad_r2_1* and exac = GRCh37; gnomad_r3* and gnomad_r4* = GRCh38) so the callset that answered is never a guess.

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. Coverage: gnomad_r4* = GRCh38 with genomes + exomes; gnomad_r3* = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.

Example Usage:

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

gnomad_get_sv_by_gene (Type: gnomADGraphQLQueryTool)#

Get structural variants (SVs) from gnomAD for a gene. The SV callset follows the requested assemb…

gnomad_get_sv_by_gene tool specification

Tool Information:

  • Name: gnomad_get_sv_by_gene

  • Type: gnomADGraphQLQueryTool

  • Description: Get structural variants (SVs) from gnomAD for a gene. The SV callset follows the requested assembly: GRCh38 (default) uses the gnomAD v4 SV callset (gnomad_sv_r4), GRCh37 uses the gnomAD v2.1 SV callset (gnomad_sv_r2_1), so SV coordinates always match the gene coordinates returned. Returns deletions, duplications, inversions, translocations, and complex SVs with population allele frequencies, SV type, consequence, and homozygote counts (null for multi-allelic CNVs). Essential for interpreting CNVs in clinical genomics.

Parameters:

  • gene_symbol (string) (required) Gene symbol (e.g., ‘BRCA1’, ‘TP53’, ‘MECP2’)

  • reference_genome (string) (optional) Reference genome assembly.

Example Usage:

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

gnomad_get_sv_by_region (Type: gnomADGraphQLQueryTool)#

Get structural variants (SVs) from gnomAD overlapping a genomic region. The SV callset follows th…

gnomad_get_sv_by_region tool specification

Tool Information:

  • Name: gnomad_get_sv_by_region

  • Type: gnomADGraphQLQueryTool

  • Description: Get structural variants (SVs) from gnomAD overlapping a genomic region. The SV callset follows the requested assembly: GRCh38 (default) uses the gnomAD v4 SV callset (gnomad_sv_r4), GRCh37 uses the gnomAD v2.1 SV callset (gnomad_sv_r2_1), so SV coordinates are always in the same assembly as the requested region. Returns DEL/DUP/INV/BND/CPX variants with allele frequencies and consequences. Use for CNV interpretation in specific chromosomal regions. Region should be < 5Mb.

Parameters:

  • chrom (string) (required) Chromosome (e.g., ‘17’, ‘X’).

  • start (integer) (required) Start position (1-based, GRCh38 by default).

  • stop (integer) (required) Stop position.

  • reference_genome (string) (optional) Reference genome assembly.

Example Usage:

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

gnomad_get_sv_detail (Type: gnomADGraphQLQueryTool)#

Get detailed information for a specific gnomAD structural variant by its ID. Resolves IDs from bo…

gnomad_get_sv_detail tool specification

Tool Information:

  • Name: gnomad_get_sv_detail

  • Type: gnomADGraphQLQueryTool

  • Description: Get detailed information for a specific gnomAD structural variant by its ID. Resolves IDs from both SV callsets, selected automatically from the ID format: GRCh38 IDs such as ‘DEL_chr17_24e4872b’ resolve against the gnomAD v4 SV callset (gnomad_sv_r4), while GRCh37 IDs such as ‘DEL_1_1937’ resolve against the gnomAD v2.1 SV callset (gnomad_sv_r2_1). Returns SV coordinates, type, length, population allele frequency, consequence, and filter status (consequence and homozygote/hemizygote counts are null for multi-allelic CNVs and intergenic SVs). Use gnomad_get_sv_by_gene or gnomad_get_sv_by_region to discover variant IDs first.

Parameters:

  • variant_id (string) (required) gnomAD structural variant ID. GRCh38/v4 IDs look like ‘DEL_chr17_24e4872b’; GRCh37/v2.1 IDs look like ‘DEL_1_1937’.

  • dataset (string) (optional) Optional SV callset override. Defaults to the callset auto-detected from the variant ID format (gnomad_sv_r2_1 for GRCh37-style IDs, gnomad_sv_r4 otherwise). Set explicitly only to query a v2.1 subset such as gnomad_sv_r2_1_controls.

Example Usage:

query = {
    "name": "gnomad_get_sv_detail",
    "arguments": {
        "variant_id": "example_value"
    }
}
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. The returned chrom/start/stop are in the assembly named by reference_genome, which gnomAD reports itself on both the transcript object and the top level of the response (GRCh38 unless the reference_genome argument says otherwise). Coordinates are not comparable across assemblies.

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. gnomad_r3 is a GENOMES-ONLY callset with no exome component, so under that default exome is null for every variant – that means ‘not present in this callset’, NOT ‘not observed in exomes’; responses carry a dataset_note saying so. Pass dataset=’gnomad_r4’ for exome allele counts (on GJB2 c.35delG that is a further 10,423 allele observations out of 1,461,600 alleles). Defaults deliberately differ across this gnomAD family: gnomad_get_variant, gnomad_search_variants and gnomad_get_region default to gnomad_r3 while gnomad_get_variant_populations and gnomad_get_constraint default to gnomad_r4, so gnomad_get_variant and gnomad_get_variant_populations report different numbers for the same variant unless you pass the same dataset to both. Every response echoes dataset and reference_genome (gnomad_r2_1* and exac = GRCh37; gnomad_r3* and gnomad_r4* = GRCh38) so the callset that answered is never a guess.

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. Coverage: gnomad_r4* = GRCh38 with genomes + exomes; gnomad_r3* = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.

Example Usage:

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

gnomad_get_variant_populations (Type: gnomADGetVariantPopulations)#

Get per-ancestry (population-stratified) allele frequencies for a variant from gnomAD by `variant…

gnomad_get_variant_populations tool specification

Tool Information:

  • Name: gnomad_get_variant_populations

  • Type: gnomADGetVariantPopulations

  • Description: Get per-ancestry (population-stratified) allele frequencies for a variant from gnomAD by variant_id (format like ‘1-55051215-G-GA’). Unlike gnomad_get_variant (aggregate AF only), this returns per-ancestry rows (amr, nfe, fin, afr, eas, sas, asj, ami, mid, remaining, plus _XX/_XY sex splits) with computed af = ac / an (af is null when an = 0), separated into genome and exome callsets. dataset defaults to gnomad_r4. Use gnomad_search_variants to find a variant_id from an rsID. gnomad_r4 carries both genomes and exomes; gnomad_r3 is genomes-only, so selecting it makes exome null for every variant (a property of the callset, not of the variant) and the response says so in dataset_note. Defaults deliberately differ across this gnomAD family: gnomad_get_variant, gnomad_search_variants and gnomad_get_region default to gnomad_r3 while gnomad_get_variant_populations and gnomad_get_constraint default to gnomad_r4, so gnomad_get_variant and gnomad_get_variant_populations report different numbers for the same variant unless you pass the same dataset to both. Every response echoes dataset and reference_genome (gnomad_r2_1* and exac = GRCh37; gnomad_r3* and gnomad_r4* = GRCh38) so the callset that answered is never a guess.

Parameters:

  • variant_id (string) (required) Variant ID (format ‘chrom-pos-ref-alt’, e.g., ‘1-55051215-G-GA’).

  • 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. Coverage: gnomad_r4* = GRCh38 with genomes + exomes; gnomad_r3* = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.

Example Usage:

query = {
    "name": "gnomad_get_variant_populations",
    "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. The response reports reference_genome, the assembly the search ran against (GRCh38 unless reference_genome says otherwise); results are assembly-specific, e.g. BRCA2 resolves to ensembl_version 17 on GRCh38 and 10 on GRCh37.

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. dataset defaults to gnomad_r3 (GRCh38, genomes only); which variants exist depends on the callset searched. Defaults deliberately differ across this gnomAD family: gnomad_get_variant, gnomad_search_variants and gnomad_get_region default to gnomad_r3 while gnomad_get_variant_populations and gnomad_get_constraint default to gnomad_r4, so gnomad_get_variant and gnomad_get_variant_populations report different numbers for the same variant unless you pass the same dataset to both. Every response echoes dataset and reference_genome (gnomad_r2_1* and exac = GRCh37; gnomad_r3* and gnomad_r4* = GRCh38) so the callset that answered is never a guess.

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. Coverage: gnomad_r4* = GRCh38 with genomes + exomes; gnomad_r3* = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.

Example Usage:

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