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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs543336253

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:142553977 (GRCh38.p14) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.0003 (2/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATR : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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
1000Genomes_30x Global Study-wide 6404 C=0.9997 T=0.0003
1000Genomes_30x African Sub 1786 C=0.9989 T=0.0011
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9996 T=0.0004
1000Genomes African Sub 1322 C=0.9985 T=0.0015
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
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.p14 chr 3 NC_000003.12:g.142553977C>G
GRCh38.p14 chr 3 NC_000003.12:g.142553977C>T
GRCh37.p13 chr 3 NC_000003.11:g.142272819C>G
GRCh37.p13 chr 3 NC_000003.11:g.142272819C>T
ATR RefSeqGene (LRG_1403) NG_008951.1:g.29850G>C
ATR RefSeqGene (LRG_1403) NG_008951.1:g.29850G>A
Gene: ATR, ATR serine/threonine kinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATR transcript variant 1 NM_001184.4:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant 1 NM_001184.4:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Asp794Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant 2 NM_001354579.2:c.2188G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Asp730His D (Asp) > H (His) Missense Variant
ATR transcript variant 2 NM_001354579.2:c.2188G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Asp730Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X1 XM_011512924.2:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant X1 XM_011512924.2:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Asp794Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X2 XM_047448360.1:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant X2 XM_047448360.1:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Asp794Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X3 XM_047448361.1:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant X3 XM_047448361.1:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Asp794Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X4 XM_011512925.2:c.2188G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Asp730His D (Asp) > H (His) Missense Variant
ATR transcript variant X4 XM_011512925.2:c.2188G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Asp730Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X5 XM_047448362.1:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant X5 XM_047448362.1:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Asp794Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X6 XM_047448363.1:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant X6 XM_047448363.1:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Asp794Asn D (Asp) > N (Asn) Missense Variant
ATR transcript variant X7 XM_047448364.1:c.2380G>C D [GAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Asp794His D (Asp) > H (His) Missense Variant
ATR transcript variant X7 XM_047448364.1:c.2380G>A D [GAT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Asp794Asn D (Asp) > N (Asn) 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.

Not Reported in ClinVar
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= G T
GRCh38.p14 chr 3 NC_000003.12:g.142553977= NC_000003.12:g.142553977C>G NC_000003.12:g.142553977C>T
GRCh37.p13 chr 3 NC_000003.11:g.142272819= NC_000003.11:g.142272819C>G NC_000003.11:g.142272819C>T
ATR RefSeqGene (LRG_1403) NG_008951.1:g.29850= NG_008951.1:g.29850G>C NG_008951.1:g.29850G>A
ATR transcript variant 1 NM_001184.4:c.2380= NM_001184.4:c.2380G>C NM_001184.4:c.2380G>A
ATR transcript variant 1 NM_001184.3:c.2380= NM_001184.3:c.2380G>C NM_001184.3:c.2380G>A
ATR transcript variant 2 NM_001354579.2:c.2188= NM_001354579.2:c.2188G>C NM_001354579.2:c.2188G>A
ATR transcript variant 2 NM_001354579.1:c.2188= NM_001354579.1:c.2188G>C NM_001354579.1:c.2188G>A
ATR transcript variant X1 XM_011512924.2:c.2380= XM_011512924.2:c.2380G>C XM_011512924.2:c.2380G>A
ATR transcript variant X1 XM_011512924.1:c.2380= XM_011512924.1:c.2380G>C XM_011512924.1:c.2380G>A
ATR transcript variant X4 XM_011512925.2:c.2188= XM_011512925.2:c.2188G>C XM_011512925.2:c.2188G>A
ATR transcript variant X4 XM_011512925.1:c.2188= XM_011512925.1:c.2188G>C XM_011512925.1:c.2188G>A
ATR transcript variant X2 XM_047448360.1:c.2380= XM_047448360.1:c.2380G>C XM_047448360.1:c.2380G>A
ATR transcript variant X3 XM_047448361.1:c.2380= XM_047448361.1:c.2380G>C XM_047448361.1:c.2380G>A
ATR transcript variant X6 XM_047448363.1:c.2380= XM_047448363.1:c.2380G>C XM_047448363.1:c.2380G>A
ATR transcript variant X5 XM_047448362.1:c.2380= XM_047448362.1:c.2380G>C XM_047448362.1:c.2380G>A
ATR transcript variant X7 XM_047448364.1:c.2380= XM_047448364.1:c.2380G>C XM_047448364.1:c.2380G>A
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Asp794= NP_001175.2:p.Asp794His NP_001175.2:p.Asp794Asn
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Asp730= NP_001341508.1:p.Asp730His NP_001341508.1:p.Asp730Asn
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Asp794= XP_011511226.1:p.Asp794His XP_011511226.1:p.Asp794Asn
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Asp730= XP_011511227.1:p.Asp730His XP_011511227.1:p.Asp730Asn
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Asp794= XP_047304316.1:p.Asp794His XP_047304316.1:p.Asp794Asn
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Asp794= XP_047304317.1:p.Asp794His XP_047304317.1:p.Asp794Asn
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Asp794= XP_047304319.1:p.Asp794His XP_047304319.1:p.Asp794Asn
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Asp794= XP_047304318.1:p.Asp794His XP_047304318.1:p.Asp794Asn
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Asp794= XP_047304320.1:p.Asp794His XP_047304320.1:p.Asp794Asn
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#.

8 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1306473339 Aug 21, 2014 (142)
2 EVA_EXAC ss1687244158 Apr 01, 2015 (144)
3 EVA_EXAC ss1687244159 Apr 01, 2015 (144)
4 GNOMAD ss2734122608 Nov 08, 2017 (151)
5 1000G_HIGH_COVERAGE ss5256300811 Oct 12, 2022 (156)
6 EVA ss5343774888 Oct 12, 2022 (156)
7 1000G_HIGH_COVERAGE ss5535882427 Oct 12, 2022 (156)
8 EVA ss5871318243 Oct 12, 2022 (156)
9 1000Genomes NC_000003.11 - 142272819 Oct 12, 2018 (152)
10 1000Genomes_30x NC_000003.12 - 142553977 Oct 12, 2022 (156)
11 ExAC

Submission ignored due to conflicting rows:
Row 7186448 (NC_000003.11:142272818:C:C 112553/112554, NC_000003.11:142272818:C:G 1/112554)
Row 7186449 (NC_000003.11:142272818:C:C 112552/112554, NC_000003.11:142272818:C:T 2/112554)

- Oct 12, 2018 (152)
12 ExAC

Submission ignored due to conflicting rows:
Row 7186448 (NC_000003.11:142272818:C:C 112553/112554, NC_000003.11:142272818:C:G 1/112554)
Row 7186449 (NC_000003.11:142272818:C:C 112552/112554, NC_000003.11:142272818:C:T 2/112554)

- Oct 12, 2018 (152)
13 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3212279 (NC_000003.11:142272818:C:C 247557/247558, NC_000003.11:142272818:C:G 1/247558)
Row 3212280 (NC_000003.11:142272818:C:C 247556/247558, NC_000003.11:142272818:C:T 2/247558)

- Jul 13, 2019 (153)
14 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3212279 (NC_000003.11:142272818:C:C 247557/247558, NC_000003.11:142272818:C:G 1/247558)
Row 3212280 (NC_000003.11:142272818:C:C 247556/247558, NC_000003.11:142272818:C:T 2/247558)

- Jul 13, 2019 (153)
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
ss1687244159, ss2734122608 NC_000003.11:142272818:C:G NC_000003.12:142553976:C:G (self)
17747343, ss1306473339, ss1687244158, ss2734122608, ss5343774888 NC_000003.11:142272818:C:T NC_000003.12:142553976:C:T (self)
23408362, ss5256300811, ss5535882427, ss5871318243 NC_000003.12:142553976:C:T NC_000003.12:142553976:C:T
Help

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

No publications for rs543336253

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.post761+d5e8e07