Ensembl Variation Ext Tools

Configuration File: ensembl_variation_ext_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

EnsemblVar_get_population_frequencies (Type: EnsemblVariationExtTool)

Get allele frequency data for a variant (SNP/indel) across global populations from gnomAD and 100…

EnsemblVar_get_population_frequencies tool specification

Tool Information:

  • Name: EnsemblVar_get_population_frequencies

  • Type: EnsemblVariationExtTool

  • Description: Get allele frequency data for a variant (SNP/indel) across global populations from gnomAD and 1000 Genomes via Ensembl. Returns allele frequencies broken down by population (e.g., gnomADe:ALL, gnomADe:nfe, 1000GENOMES:phase_3:CEU, etc.). Essential for assessing variant rarity in different ethnic groups, interpreting clinical significance, and population genetics studies. Example: rs429358 (APOE epsilon-4 allele) shows C allele frequency of 14.8% globally (gnomAD), 22.7% in African populations, 9.8% in East Asian populations.

Parameters:

  • variant_id (string) (required) dbSNP rsID of the variant. Examples: ‘rs429358’ (APOE), ‘rs7903146’ (TCF7L2), ‘rs1042779’.

  • species (string) (optional) Species name. Default ‘human’. Examples: ‘human’, ‘homo_sapiens’.

Example Usage:

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

EnsemblVar_get_variant_consequences (Type: EnsemblVariationExtTool)

Get detailed variant information including consequence type, clinical significance, synonyms, evi…

EnsemblVar_get_variant_consequences tool specification

Tool Information:

  • Name: EnsemblVar_get_variant_consequences

  • Type: EnsemblVariationExtTool

  • Description: Get detailed variant information including consequence type, clinical significance, synonyms, evidence attributes, and allele mappings from Ensembl. More comprehensive than VEP - returns the full variant record with all known synonyms, mapped positions, ancestral allele, and minor allele data. Example: rs429358 returns most_severe_consequence=’missense_variant’, 27 synonyms, mapped to chr19:44908684 (GRCh38), and is classified as a missense_variant affecting APOE.

Parameters:

  • variant_id (string) (required) dbSNP rsID of the variant. Examples: ‘rs429358’ (APOE), ‘rs7903146’ (TCF7L2), ‘rs1042779’.

  • species (string) (optional) Species name. Default ‘human’. Examples: ‘human’, ‘homo_sapiens’.

Example Usage:

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