dbsnp.clinvar_accessions

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('dbsnp.clinvar_accessions')
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()

Out[1]:

	sources	build	assembly_accession	assembly_name	chromosome	position	ref_allele	alt_allele	rsid	clinvar_accession	clinvar_significance	clinvar_review_status
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	69134	A	G	rs781394307	RCV004071174.1	[Likely benign]	single
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	69314	T	G	rs2521653848	RCV004496909.1	[Uncertain significance]	single
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	69423	G	A	rs2521654033	RCV004496910.1	[Uncertain significance]	single
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	69581	C	G	rs1570409925	RCV004109876.1	[Uncertain significance]	single
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	69682	G	A	rs766444643	RCV004230996.1	[Uncertain significance]	single

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("dbsnp.clinvar_accessions")
df <- filter(lf, assembly_accession == "GCF_000001405.25", chromosome == "1") |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 12 columns)
   assembly_accession | chromosome | build | assembly_name | position | ref_allele | alt_allele | rsid
   ------------------ | ---------- | ----- | ------------- | -------- | ---------- | ---------- | ------------
0  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 69134    | A          | G          | rs781394307
1  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 69314    | T          | G          | rs2521653848
2  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 69423    | G          | A          | rs2521654033
3  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 69581    | C          | G          | rs1570409925
4  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 69682    | G          | A          | rs766444643

Description

ClinVar accessions and classifications associated with dbSNP variants.

An RCV accession aggregates submissions for a variant and condition set.

Individual SCV assertions are not included.

Use clinvar_diseases and clinvar_disease_xrefs for the reported conditions and their identifiers.

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

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).
ref_allele	TEXT	Reference allele.
alt_allele	TEXT	Alternate allele.
rsid	TEXT	NCBI RefSNP identifier.
clinvar_accession	TEXT	ClinVar RCV accession with version (e.g. RCV001326669.6), identifying the aggregate record for this variant and condition set.
clinvar_significance	TEXT[]	ClinVar clinical significance labels reported for the accession.
clinvar_review_status	TEXT	ClinVar review status code for the accession.