ClinVar Clinical Significance: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Retrieve ClinVar clinical significance

dnakit.databases.clin_var_get_clinical_significance(*, variant_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
variant_id	string	Required	ClinVar variant ID (e.g., '12345', '123456')
verbose	bool	True	Progress flag.

Retrieve ClinVar variant summaries and review status

dnakit.databases.clin_var_get_variant_details(*, variant_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
variant_id	string	Required	ClinVar variant ID (e.g., '12345', '123456')
verbose	bool	True	Progress flag.

Search ClinVar variants by gene, disease or identifier

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)

Parameter	Type	Required / default	Description and constraints
gene	string	None	Gene name or symbol (e.g., 'BRCA1', 'BRCA2') At least one of gene, condition, or variant_id must be provided.
condition	string	None	Disease or condition name (e.g., 'breast cancer', 'diabetes') At least one of gene, condition, or variant_id must be provided. Matched against ClinVar's disease index, which carries MedGen's own condition names exactly -- a synonym, a locus name or a misspelling ('Lebers congenital amaurosis' for the indexed 'Leber congenital amaurosis') matches nothing there, so the search falls back to an unrestricted free-text match. When that happens the response says so: 'condition_filter_applied': false plus a 'condition_filter_warning', meaning total_count is NOT a disease-filtered count. Use MedGen_search_conditions to get the indexed name.
variant_id	string	None	ClinVar variant ID (e.g., '12345') At least one of gene, condition, or variant_id must be provided.
variant_name	string | array | null	None	Protein change or HGVS notation to search for (e.g., 'Glu6Val', 'V600E', 'c.20A>T'), matched against ClinVar's own [Variant name] index -- combine with 'gene' for an exact-match lookup of a specific known variant instead of browsing all of a gene's ClinVar entries. A gene-level browse can silently miss well-known but old/low-ID records once a gene has more entries than max_results (e.g. HBB's canonical sickle-cell record, NM_000518.5(HBB):c.20A>T (p.Glu7Val), isn't within the first 100-425 gene-level rows). Accepts a list to try multiple candidate names in one call (e.g. every allele at a multi-allelic site) -- combined with OR.
max_results	integer	None	Maximum number of results to return (default: 20). Alias: limit.
limit	integer	None	Alias for max_results: maximum number of results to return.
clinical_significance	string	None	Filter by clinical significance. Must be one of the classes ClinVar's index actually recognizes: 'Pathogenic', 'Likely pathogenic', 'Uncertain significance', 'VUS', 'Likely benign', 'Benign', 'Established risk allele', 'Likely risk allele', 'Uncertain risk allele', 'drug response', 'risk factor', 'not provided', 'other'. Case-insensitive; underscores/hyphens are treated as spaces. Combine two classes with '/' to search their union (e.g. 'Pathogenic/Likely pathogenic'). Any other value is rejected with an error rather than silently filtering the results to nothing.
gene_symbol	string | null	None	Alias for gene. HGNC gene symbol (e.g., "DPYD", "CYP2C19").
significance	string | null	None	Alias for clinical_significance (e.g., "pathogenic", "benign", "uncertain_significance"). Same accepted value set and same validation as clinical_significance.
query	string | null	None	Alias for condition. Free-text search mapped to condition/disease field.
variant	string | array | null	None	DNAKit optional alias for variant_name
verbose	bool	True	Progress flag.