ClinVar Clinical Significance¶

See the FAQ for dependencies and return conventions.

1) ClinVar variant search¶

Purpose: Search ClinVar by gene, condition, ClinVar ID, HGVS, or protein change.
Method: Search ClinVar with the supplied filters and result limit.
API: dnakit.annotation.search_clinvar_variants(gene[optional], condition[optional], variant_id[optional], variant_name[optional], clinical_significance[optional], limit[optional])
Input: At least one search field; limit must be 1–100.
Output: Returns ProviderResult with query content in data, plus provider and provenance.
Example code:

from dnakit.annotation import search_clinvar_variants

result = search_clinvar_variants(gene="TP53", variant_name="c.215C>G", limit=10)
print(result.data)

Example output: ClinVar identifiers and summary records.

2) ClinVar variant details¶

Purpose: Retrieve accession, gene, coordinates, and review status for one ClinVar variation.
Method: Retrieve the ClinVar detail record by variation ID.
API: dnakit.annotation.get_clinvar_variant(variant_id[required])
Input: A ClinVar variation ID such as 12345.
Output: Returns ProviderResult with query content in data, plus provider and provenance.
Example code:

from dnakit.annotation import get_clinvar_variant

result = get_clinvar_variant("12345")
print(result.data)

Example output: ClinVar variant details.

3) ClinVar clinical significance¶

Purpose: Retrieve clinical-significance assertions for one ClinVar variation.
Method: Read clinical significance and interpretation from the selected ClinVar record.
API: dnakit.annotation.get_clinvar_significance(variant_id[required])
Input: A ClinVar variation ID.
Output: Returns ProviderResult with query content in data, plus provider and provenance.
Example code:

from dnakit.annotation import get_clinvar_significance

result = get_clinvar_significance("12345")
print(result.data)

Example output: Pathogenicity classifications and clinical interpretations.

4) Retrieve ClinVar clinical significance¶

Purpose: Retrieve ClinVar clinical significance.
Method: Use ClinVarGetClinicalSignificance to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_var_get_clinical_significance(*, variant_id, verbose=True)
Input: Provide variant_id.
Output: Returns a mapping with status, data, variant_id, url and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_var_get_clinical_significance(
    variant_id='12345',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "status": "<string>",
  "data": {
    "variant_id": "<string>",
    "germline_classification": {
      "description": "<string>",
      "review_status": "<string>",
      "last_evaluated": "<string>",
      "fda_recognized": "<string>",
      "traits": "<array>"
    },
    "clinical_impact": {
      "description": "<string>",
      "review_status": "<string>",
      "last_evaluated": "<string>"
    },
    "oncogenicity": {
      "description": "<string>",
      "review_status": "<string>",
      "last_evaluated": "<string>"
    },
    "raw_data": "<object>"
  },
  "variant_id": "<string>",
  "url": "<string>"
}

Full parameters and usage notes

5) Retrieve ClinVar variant summaries and review status¶

Purpose: Retrieve ClinVar variant summaries and review status.
Method: Use ClinVarGetVariantDetails to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_var_get_variant_details(*, variant_id, verbose=True)
Input: Provide variant_id.
Output: Returns a mapping with status, data, variant_id, url and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_var_get_variant_details(
    variant_id='12345',
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "status": "<string>",
  "data": {
    "variant_id": "<string>",
    "accession": "<string>",
    "obj_type": "<string>",
    "chromosome": "<string>",
    "location": "<string>",
    "variation_name": "<string>",
    "title": "<string>",
    "genes": [
      "<string>"
    ]
  },
  "variant_id": "<string>",
  "url": "<string>"
}

Full parameters and usage notes

6) Search ClinVar variants by gene, disease or identifier¶

Purpose: Search ClinVar variants by gene, disease or identifier.
Method: Use ClinVarSearchVariants to query or submit the supplied input and parse the response.
API： dnakit.databases.clin_var_search_variants(*, gene=None, condition=None, variant_id=None, variant_name=None, max_results=None, limit=None, clinical_significance=None, gene_symbol=None, significance=None, query=None, variant=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a mapping with status, data, search_params, url and related fields.
Example code:

import dnakit

result = dnakit.databases.clin_var_search_variants(
    gene='BRCA1',
    max_results=10,
    verbose=False,
)
print(result)

Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "status": "<string>",
  "data": {
    "esearchresult": {
      "count": "<string>",
      "idlist": "<array>",
      "querytranslation": "<string>"
    }
  },
  "search_params": {
    "gene": "<string>",
    "condition": "<string>",
    "variant_id": "<string>"
  },
  "url": "<string>"
}

Full parameters and usage notes