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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs571264557

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:26696761 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.005954 (1576/264690, TOPMED)
T=0.005722 (795/138938, GnomAD)
T=0.00027 (4/14766, GnomAD_exome) (+ 5 more)
T=0.00451 (65/14420, ALFA)
T=0.0046 (23/5008, 1000G)
T=0.001 (1/984, ExAC)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ARID1A : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 1 NC_000001.11:g.26696761C>T
GRCh37.p13 chr 1 NC_000001.10:g.27023252C>T
ARID1A RefSeqGene (LRG_875) NG_029965.1:g.5731C>T
Gene: ARID1A, AT-rich interaction domain 1A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ARID1A transcript variant 1 NM_006015.6:c.358C>T P [CCG] > S [TCG] Coding Sequence Variant
AT-rich interactive domain-containing protein 1A isoform a NP_006006.3:p.Pro120Ser P (Pro) > S (Ser) Missense Variant
ARID1A transcript variant 2 NM_139135.4:c.358C>T P [CCG] > S [TCG] Coding Sequence Variant
AT-rich interactive domain-containing protein 1A isoform b NP_624361.1:p.Pro120Ser P (Pro) > S (Ser) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 427771 )
ClinVar Accession Disease Names Clinical Significance
RCV000503505.1 not specified Uncertain-Significance

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14420 C=0.99549 T=0.00451
European Sub 9824 C=1.0000 T=0.0000
African Sub 2946 C=0.9793 T=0.0207
African Others Sub 114 C=0.956 T=0.044
African American Sub 2832 C=0.9802 T=0.0198
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.993 T=0.007
Latin American 2 Sub 610 C=0.997 T=0.003
South Asian Sub 98 C=1.00 T=0.00
Other Sub 684 C=0.999 T=0.001


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.994046 T=0.005954
gnomAD - Genomes Global Study-wide 138938 C=0.994278 T=0.005722
gnomAD - Genomes European Sub 75220 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 41606 C=0.98164 T=0.01836
gnomAD - Genomes American Sub 13566 C=0.99830 T=0.00170
gnomAD - Genomes Ashkenazi Jewish Sub 3314 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3108 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2124 C=0.9962 T=0.0038
gnomAD - Exomes Global Study-wide 14766 C=0.99973 T=0.00027
gnomAD - Exomes European Sub 9390 C=1.0000 T=0.0000
gnomAD - Exomes Asian Sub 3204 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 1072 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 696 C=0.999 T=0.001
gnomAD - Exomes Other Sub 294 C=1.000 T=0.000
gnomAD - Exomes African Sub 110 C=0.973 T=0.027
Allele Frequency Aggregator Total Global 14420 C=0.99549 T=0.00451
Allele Frequency Aggregator European Sub 9824 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2946 C=0.9793 T=0.0207
Allele Frequency Aggregator Other Sub 684 C=0.999 T=0.001
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.997 T=0.003
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.993 T=0.007
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=0.9954 T=0.0046
1000Genomes African Sub 1322 C=0.9826 T=0.0174
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
ExAC Global Study-wide 984 C=0.999 T=0.001
ExAC Asian Sub 752 C=1.000 T=0.000
ExAC Europe Sub 192 C=1.000 T=0.000
ExAC African Sub 24 C=0.96 T=0.04
ExAC Other Sub 10 C=1.0 T=0.0
ExAC American Sub 6 C=1.0 T=0.0
SGDP_PRJ Global Study-wide 4 C=0.5 T=0.5
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T
GRCh38.p13 chr 1 NC_000001.11:g.26696761= NC_000001.11:g.26696761C>T
GRCh37.p13 chr 1 NC_000001.10:g.27023252= NC_000001.10:g.27023252C>T
ARID1A RefSeqGene (LRG_875) NG_029965.1:g.5731= NG_029965.1:g.5731C>T
ARID1A transcript variant 1 NM_006015.6:c.358= NM_006015.6:c.358C>T
ARID1A transcript variant 1 NM_006015.5:c.358= NM_006015.5:c.358C>T
ARID1A transcript variant 1 NM_006015.4:c.358= NM_006015.4:c.358C>T
ARID1A transcript variant 2 NM_139135.4:c.358= NM_139135.4:c.358C>T
ARID1A transcript variant 2 NM_139135.3:c.358= NM_139135.3:c.358C>T
ARID1A transcript variant 2 NM_139135.2:c.358= NM_139135.2:c.358C>T
ARID1A transcript variant 3 NM_018450.4:c.358= NM_018450.4:c.358C>T
AT-rich interactive domain-containing protein 1A isoform a NP_006006.3:p.Pro120= NP_006006.3:p.Pro120Ser
AT-rich interactive domain-containing protein 1A isoform b NP_624361.1:p.Pro120= NP_624361.1:p.Pro120Ser
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

13 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1290126657 Aug 21, 2014 (142)
2 EVA_EXAC ss1685410332 Apr 01, 2015 (144)
3 ILLUMINA ss1958255604 Feb 12, 2016 (147)
4 TOPMED ss2323101950 Dec 20, 2016 (150)
5 GNOMAD ss2731282804 Nov 08, 2017 (151)
6 GNOMAD ss2746267632 Nov 08, 2017 (151)
7 GNOMAD ss2752935029 Nov 08, 2017 (151)
8 ILLUMINA ss3021069269 Nov 08, 2017 (151)
9 TOPMED ss3071550964 Nov 08, 2017 (151)
10 ILLUMINA ss3651394720 Oct 11, 2018 (152)
11 KHV_HUMAN_GENOMES ss3798988231 Jul 12, 2019 (153)
12 SGDP_PRJ ss3848458127 Apr 25, 2020 (154)
13 TOPMED ss4442931974 Apr 27, 2021 (155)
14 1000Genomes NC_000001.10 - 27023252 Oct 11, 2018 (152)
15 ExAC NC_000001.10 - 27023252 Oct 11, 2018 (152)
16 gnomAD - Genomes NC_000001.11 - 26696761 Apr 27, 2021 (155)
17 gnomAD - Exomes NC_000001.10 - 27023252 Jul 12, 2019 (153)
18 SGDP_PRJ NC_000001.10 - 27023252 Apr 25, 2020 (154)
19 TopMed NC_000001.11 - 26696761 Apr 27, 2021 (155)
20 ALFA NC_000001.11 - 26696761 Apr 27, 2021 (155)
21 ClinVar RCV000503505.1 Oct 11, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
817941, 4596989, 297184, 475107, ss1290126657, ss1685410332, ss1958255604, ss2323101950, ss2731282804, ss2746267632, ss2752935029, ss3021069269, ss3651394720, ss3848458127 NC_000001.10:27023251:C:T NC_000001.11:26696760:C:T (self)
RCV000503505.1, 5731075, 4113636, 6538309, 1692695287, ss3071550964, ss3798988231, ss4442931974 NC_000001.11:26696760:C:T NC_000001.11:26696760:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs571264557
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad