Clingen Ar Tools

Configuration File: clingen_ar_tools.json Tool Type: Local Tools Count: 3

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)

ClinGenAR_lookup_by_external_id (Type: ClinGenARTool)

Reverse-lookup the ClinGen Allele Registry by an external identifier. Given a dbSNP rsID (dbsnp_r…

ClinGenAR_lookup_by_external_id tool specification

Tool Information:

  • Name: ClinGenAR_lookup_by_external_id

  • Type: ClinGenARTool

  • Description: Reverse-lookup the ClinGen Allele Registry by an external identifier. Given a dbSNP rsID (dbsnp_rs) or a ClinVar VariationID (clinvar_variation_id), resolves it to the canonical ClinGen allele (CA id) and returns ALL cross-references (ClinVar alleles/variations, dbSNP, COSMIC, gnomAD, MyVariantInfo) plus the community standard HGVS title and genomic allele HGVS. This complements ClinGenAR_lookup_allele (which takes an HGVS expression): use this when you start from an rsID or ClinVar variation id instead of HGVS. Example: dbsnp_rs=113488022 -> CA123643, ‘NM_004333.6(BRAF):c.1799T>A (p.Val600Glu)’, incl COSM476; clinvar_variation_id=13961 resolves to the same CA123643 record. Public API, no key required.

Parameters:

  • dbsnp_rs ([‘string’, ‘integer’, ‘null’]) (optional) dbSNP rsID to resolve. The ‘rs’ prefix is optional (e.g. 113488022 or ‘rs113488022’). Mutually exclusive with clinvar_variation_id.

  • clinvar_variation_id ([‘string’, ‘integer’, ‘null’]) (optional) ClinVar VariationID to resolve (e.g. 13961). Mutually exclusive with dbsnp_rs.

Example Usage:

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