Skip to content
bedrock.bio

dbsnp.variants

import bedrock_bio as bb

rel = bb.load_table('dbsnp.variants')
rel = rel.filter("assembly_accession = 'GCF_000001405.25' AND chromosome = '1'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources build assembly_accession assembly_name chromosome position rsid ref_allele alt_allele qual ... in_acceptor_splice_site in_donor_splice_site in_intron in_3_prime_gene in_5_prime_gene has_genotypes_available in_publication is_common clinvar_hgvs_name clinvar_allele_origin
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc... b157 GCF_000001405.25 GRCh37.p13 1 10001 rs1570391677 T A None ... False False False False True True False True None <NA>
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc... b157 GCF_000001405.25 GRCh37.p13 1 10001 rs1570391677 T C None ... False False False False True True False True None <NA>
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc... b157 GCF_000001405.25 GRCh37.p13 1 10002 rs1570391692 A C None ... False False False False True True False False None <NA>
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc... b157 GCF_000001405.25 GRCh37.p13 1 10003 rs1570391694 A C None ... False False False False True True False False None <NA>
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc... b157 GCF_000001405.25 GRCh37.p13 1 10007 rs1639538116 T C None ... False False False False True True False False None <NA>

Description

Section titled “Description”

dbSNP variants and their annotations.

Functional class flags are true when any alternate allele has that annotation.

ClinVar fields here are variant-level; use the clinvar_* tables for detailed ClinVar records.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
  • chromosome
    • '1'
    • '10'
    • '11'
    • '12'
    • '13'
    • '14'
    • '15'
    • '16'
    • '17'
    • '18'
    • '19'
    • '2'
    • '20'
    • '21'
    • '22'
    • '3'
    • '4'
    • '5'
    • '6'
    • '7'
    • '8'
    • '9'
    • 'MT'
    • 'X'
    • 'Y'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Source provenance for the row.
build TEXT dbSNP build version (e.g. b157).
assembly_accession TEXT Partition column. Versioned RefSeq assembly accession (GCF) for the variant coordinates.
assembly_name TEXT Exact NCBI assembly name, including its patch release (for example, GRCh38.p14).
chromosome TEXT Partition column. Chromosome on which the variant is located (1-22, X, Y, MT).
position INT Variant position within the chromosome (1-based).
rsid TEXT NCBI RefSNP identifier, such as rs7412.
ref_allele TEXT Reference allele.
alt_allele TEXT Alternate allele.
qual TEXT Variant quality score; null when not provided.
filter TEXT Variant filter status; null when not provided.
first_dbsnp_build TEXT First dbSNP build in which the rsID appeared (e.g. 150). Null for rsIDs created from frequency data without submitted SNPs.
allele_origin TEXT Variant allele origin — one of unspecified, Germline, Somatic, Both. Null when not provided.
suspect_reasons TEXT[] Variant suspect reason codes, decoded to labels — any of unspecified, Paralog, byEST, oldAlign, Para_EST, 1kg_failed, or other. A variant may carry more than one.
variation_class TEXT Variation class (SNV, INS, DEL, INDEL, or MNV).
is_precious BOOLEAN Whether dbSNP marks the variant as clinically significant or cited in PubMed.
has_non_synonymous_frameshift BOOLEAN Has nonsynonymous frameshift — a coding-region variation where one allele in the set changes all downstream amino acids.
has_non_synonymous_missense BOOLEAN Has nonsynonymous missense — a coding-region variation where one allele in the set changes the protein peptide.
has_non_synonymous_nonsense BOOLEAN Has nonsynonymous nonsense — a coding-region variation where one allele in the set changes to a STOP codon (TER).
has_synonymous BOOLEAN Has synonymous — a coding-region variation where one allele in the set does not change the encoded amino acid.
in_3_prime_utr BOOLEAN Location is in a 3’ untranslated region (UTR).
in_5_prime_utr BOOLEAN Location is in a 5’ untranslated region (UTR).
in_acceptor_splice_site BOOLEAN In acceptor splice site.
in_donor_splice_site BOOLEAN In donor splice site.
in_intron BOOLEAN In intron.
in_3_prime_gene BOOLEAN In 3’ gene region.
in_5_prime_gene BOOLEAN In 5’ gene region.
has_genotypes_available BOOLEAN Genotypes available.
in_publication BOOLEAN RefSNP or associated SubSNP is mentioned in a publication.
is_common BOOLEAN Whether the RefSNP is a common SNP — one with at least one 1000 Genomes population whose minor allele frequency is >= 1% and for which at least two founders contribute to that frequency.
clinvar_hgvs_name TEXT ClinVar HGVS name for this variant (e.g. NC_000019.10:g.44908822C>T). Null when the variant has no ClinVar record.
clinvar_allele_origin TEXT[][] ClinVar allele origin categories, grouped per alternate allele, if present.