Variant Records and Population Frequencies: 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 dbSNP allele frequencies

dnakit.databases.dbsnp_get_frequencies(*, rsid, verbose=True)

Parameter	Type	Required / default	Description and constraints
rsid	string	Required	dbSNP rsID (e.g., 'rs12345', '12345')
verbose	bool	True	Progress flag.

Retrieve dbSNP coordinates and alleles by rsID

dnakit.databases.dbsnp_get_variant_by_rsid(*, rsid, verbose=True)

Parameter	Type	Required / default	Description and constraints
rsid	string	Required	dbSNP rsID (e.g., 'rs12345', '12345')
verbose	bool	True	Progress flag.

Retrieve gnomAD gene constraint metrics

dnakit.databases.gnomad_get_gene_constraints(*, gene_symbol, reference_genome=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	Required	Gene symbol (e.g., 'BRCA1', 'TP53')
reference_genome	string	None	Reference genome.
verbose	bool	True	Progress flag.

Retrieve gnomAD variant metadata

dnakit.databases.gnomad_get_variant(*, variant_id, dataset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
variant_id	string	Required	Variant ID (e.g., '19-44908822-C-T').
dataset	string	None	gnomAD dataset ID. Allowed values: gnomad_r4, gnomad_r4_non_ukb, gnomad_r3, gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2, gnomad_r2_1, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed, exac. Coverage: gnomad_r4 = GRCh38 with genomes + exomes; gnomad_r3 = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.
verbose	bool	True	Progress flag.

Retrieve ancestry-specific gnomAD allele frequencies

dnakit.databases.gnomad_get_variant_populations(*, variant_id, dataset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
variant_id	string	Required	Variant ID (format 'chrom-pos-ref-alt', e.g., '1-55051215-G-GA').
dataset	string	None	gnomAD dataset ID. Allowed values: gnomad_r4, gnomad_r4_non_ukb, gnomad_r3, gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2, gnomad_r2_1, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed, exac. Coverage: gnomad_r4 = GRCh38 with genomes + exomes; gnomad_r3 = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.
verbose	bool	True	Progress flag.

Search gnomAD variant identifiers

dnakit.databases.gnomad_search_variants(*, query=None, dataset=None, variant=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	None	Variant search query (e.g., 'rs7412').
dataset	string	None	gnomAD dataset ID. Allowed values: gnomad_r4, gnomad_r4_non_ukb, gnomad_r3, gnomad_r3_controls_and_biobanks, gnomad_r3_non_cancer, gnomad_r3_non_neuro, gnomad_r3_non_topmed, gnomad_r3_non_v2, gnomad_r2_1, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed, exac. Coverage: gnomad_r4 = GRCh38 with genomes + exomes; gnomad_r3 = GRCh38 with genomes ONLY (no exome component, so exome is always null); gnomad_r2_1* = GRCh37 with genomes + exomes; exac = GRCh37 with exomes only.
variant	string	None	DNAKit optional alias for query
verbose	bool	True	Progress flag.