Clingen Allele Tools#

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

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

Available Tools#

ClinGenAllele_get_allele (Type: ClinGenAlleleTool)#

Get detailed information for a canonical allele by its ClinGen Allele Registry CA ID. Returns cro…

ClinGenAllele_get_allele tool specification

Tool Information:

  • Name: ClinGenAllele_get_allele

  • Type: ClinGenAlleleTool

  • Description: Get detailed information for a canonical allele by its ClinGen Allele Registry CA ID. Returns cross-references to ClinVar, dbSNP, COSMIC, gnomAD, genomic coordinates, and transcript-level HGVS expressions. COORDINATES: every genomic_alleles row reports start/end in 0-based interbase (half-open) form and carries a ‘coordinate_system’ field saying so; the 1-based genomic position used by HGVS, VCF and gnomAD is start+1 (e.g. start 32332711 = g.32332712). Each row also carries ‘reference_sequence’, the registry RefSeq URI (e.g. http://reg.genome.network/refseq/RS000061) identifying the sequence the coordinates are counted against - for RefSeqGene/LRG rows that have no reference_genome and no chromosome, this is the only field identifying the coordinate frame.

Parameters:

  • ca_id ([‘string’, ‘null’]) (optional) ClinGen canonical allele identifier (e.g., ‘CA000387’). Obtain from ClinGenAllele_lookup_hgvs or ClinVar.

  • allele_id ([‘string’, ‘null’]) (optional) Alias for ca_id. ClinGen canonical allele identifier (e.g., ‘CA000387’).

Example Usage:

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

ClinGenAllele_lookup_hgvs (Type: ClinGenAlleleTool)#

Look up a genetic variant by HGVS expression in the ClinGen Allele Registry to get its canonical …

ClinGenAllele_lookup_hgvs tool specification

Tool Information:

  • Name: ClinGenAllele_lookup_hgvs

  • Type: ClinGenAlleleTool

  • Description: Look up a genetic variant by HGVS expression in the ClinGen Allele Registry to get its canonical allele identifier (CA ID) and cross-references to ClinVar, dbSNP, COSMIC, gnomAD, and other databases. Accepts genomic (NC_*), coding (NM_*), or protein (NP_*) HGVS expressions. COORDINATES: every genomic_alleles row reports start/end in 0-based interbase (half-open) form and carries a ‘coordinate_system’ field saying so; the 1-based genomic position used by HGVS, VCF and gnomAD is start+1 (e.g. start 32332711 = g.32332712). Each row also carries ‘reference_sequence’, the registry RefSeq URI (e.g. http://reg.genome.network/refseq/RS000061) identifying the sequence the coordinates are counted against - for RefSeqGene/LRG rows that have no reference_genome and no chromosome, this is the only field identifying the coordinate frame.

Parameters:

  • hgvs (string) (required) HGVS expression for the variant. Examples: ‘NC_000017.11:g.7674220C>T’ (genomic), ‘NM_000546.6:c.743G>A’ (coding). Must use a valid reference sequence accession.

Example Usage:

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