Clingen Ar Tools

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

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

Available Tools

ClinGenAR_get_external_records (Type: ClinGenARTool)

Get detailed cross-references and external database records for a ClinGen canonical allele. Takes…

ClinGenAR_get_external_records tool specification

Tool Information:

  • Name: ClinGenAR_get_external_records

  • Type: ClinGenARTool

  • Description: Get detailed cross-references and external database records for a ClinGen canonical allele. Takes a ClinGen allele ID (CA ID) and returns links to ClinVar, dbSNP, COSMIC, gnomAD, ExAC, and other databases. Useful for finding all known database entries for a given variant. Example: CA000387 (TP53 R248Q) returns ClinVar variation IDs, COSMIC IDs, dbSNP rsIDs, and gnomAD allele frequencies.

Parameters:

  • allele_id (string) (required) ClinGen canonical allele ID. Examples: ‘CA000387’ (TP53 R248Q), ‘CA006116’ (BRCA1 variant). Use ClinGenAR_lookup_allele first to get the CA ID.

Example Usage:

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

ClinGenAR_lookup_allele (Type: ClinGenARTool)

Look up a genetic variant in the ClinGen Allele Registry by HGVS notation. Returns the canonical …

ClinGenAR_lookup_allele tool specification

Tool Information:

  • Name: ClinGenAR_lookup_allele

  • Type: ClinGenARTool

  • Description: Look up a genetic variant in the ClinGen Allele Registry by HGVS notation. Returns the canonical allele identifier (CA ID), community standard title, and cross-references to ClinVar, dbSNP, COSMIC, gnomAD, and other databases. The Allele Registry normalizes variant representations across different coordinate systems and nomenclatures. Example: ‘NM_000546.6:c.743G>A’ returns CA000387 (TP53 p.Arg248Gln) with links to ClinVar, COSMIC, and gnomAD.

Parameters:

  • hgvs (string) (required) HGVS expression for the variant. Supports coding (c.), genomic (g.), and protein (p.) notations. Examples: ‘NM_000546.6:c.743G>A’ (TP53 R248Q), ‘NC_000017.11:g.7674220C>T’, ‘NM_000059.4:c.5946delT’ (BRCA2).

Example Usage:

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