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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.

rs778148931

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:142547844 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000008 (2/264690, TOPMED)
G=0.000028 (7/251198, GnomAD_exome)
G=0.000025 (3/121208, ExAC) (+ 1 more)
G=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATR : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 10680 A=1.00000 G=0.00000
European Sub 6962 A=1.0000 G=0.0000
African Sub 2294 A=1.0000 G=0.0000
African Others Sub 84 A=1.00 G=0.00
African American Sub 2210 A=1.0000 G=0.0000
Asian Sub 108 A=1.000 G=0.000
East Asian Sub 84 A=1.00 G=0.00
Other Asian Sub 24 A=1.00 G=0.00
Latin American 1 Sub 146 A=1.000 G=0.000
Latin American 2 Sub 610 A=1.000 G=0.000
South Asian Sub 94 A=1.00 G=0.00
Other Sub 466 A=1.000 G=0.000


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 A=0.999992 G=0.000008
gnomAD - Exomes Global Study-wide 251198 A=0.999972 G=0.000028
gnomAD - Exomes European Sub 135210 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48994 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34544 A=0.99980 G=0.00020
gnomAD - Exomes African Sub 16256 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6120 A=1.0000 G=0.0000
ExAC Global Study-wide 121208 A=0.999975 G=0.000025
ExAC Europe Sub 73256 A=1.00000 G=0.00000
ExAC Asian Sub 25152 A=1.00000 G=0.00000
ExAC American Sub 11500 A=0.99974 G=0.00026
ExAC African Sub 10396 A=1.00000 G=0.00000
ExAC Other Sub 904 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 10680 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 6962 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2294 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 466 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 G=0.00
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.142547844A>C
GRCh38.p14 chr 3 NC_000003.12:g.142547844A>G
GRCh38.p14 chr 3 NC_000003.12:g.142547844A>T
GRCh37.p13 chr 3 NC_000003.11:g.142266686A>C
GRCh37.p13 chr 3 NC_000003.11:g.142266686A>G
GRCh37.p13 chr 3 NC_000003.11:g.142266686A>T
ATR RefSeqGene (LRG_1403) NG_008951.1:g.35983T>G
ATR RefSeqGene (LRG_1403) NG_008951.1:g.35983T>C
ATR RefSeqGene (LRG_1403) NG_008951.1:g.35983T>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.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Leu1080Val L (Leu) > V (Val) Missense Variant
ATR transcript variant 1 NM_001184.4:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant 1 NM_001184.4:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Leu1080Met L (Leu) > M (Met) Missense Variant
ATR transcript variant 2 NM_001354579.2:c.3046T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Leu1016V…

NP_001341508.1:p.Leu1016Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant 2 NM_001354579.2:c.3046T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Leu1016= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant 2 NM_001354579.2:c.3046T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Leu1016M…

NP_001341508.1:p.Leu1016Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X1 XM_011512924.2:c.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Leu1080V…

XP_011511226.1:p.Leu1080Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X1 XM_011512924.2:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X1 XM_011512924.2:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Leu1080M…

XP_011511226.1:p.Leu1080Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X2 XM_047448360.1:c.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Leu1080V…

XP_047304316.1:p.Leu1080Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X2 XM_047448360.1:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X2 XM_047448360.1:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Leu1080M…

XP_047304316.1:p.Leu1080Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X3 XM_047448361.1:c.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Leu1080V…

XP_047304317.1:p.Leu1080Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X3 XM_047448361.1:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X3 XM_047448361.1:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Leu1080M…

XP_047304317.1:p.Leu1080Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X4 XM_011512925.2:c.3046T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Leu1016V…

XP_011511227.1:p.Leu1016Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X4 XM_011512925.2:c.3046T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Leu1016= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X4 XM_011512925.2:c.3046T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Leu1016M…

XP_011511227.1:p.Leu1016Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X5 XM_047448362.1:c.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Leu1080V…

XP_047304318.1:p.Leu1080Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X5 XM_047448362.1:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X5 XM_047448362.1:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Leu1080M…

XP_047304318.1:p.Leu1080Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X6 XM_047448363.1:c.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Leu1080V…

XP_047304319.1:p.Leu1080Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X6 XM_047448363.1:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X6 XM_047448363.1:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Leu1080M…

XP_047304319.1:p.Leu1080Met

L (Leu) > M (Met) Missense Variant
ATR transcript variant X7 XM_047448364.1:c.3238T>G L [TTG] > V [GTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Leu1080V…

XP_047304320.1:p.Leu1080Val

L (Leu) > V (Val) Missense Variant
ATR transcript variant X7 XM_047448364.1:c.3238T>C L [TTG] > L [CTG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Leu1080= L (Leu) > L (Leu) Synonymous Variant
ATR transcript variant X7 XM_047448364.1:c.3238T>A L [TTG] > M [ATG] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Leu1080M…

XP_047304320.1:p.Leu1080Met

L (Leu) > M (Met) 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 A= C G T
GRCh38.p14 chr 3 NC_000003.12:g.142547844= NC_000003.12:g.142547844A>C NC_000003.12:g.142547844A>G NC_000003.12:g.142547844A>T
GRCh37.p13 chr 3 NC_000003.11:g.142266686= NC_000003.11:g.142266686A>C NC_000003.11:g.142266686A>G NC_000003.11:g.142266686A>T
ATR RefSeqGene (LRG_1403) NG_008951.1:g.35983= NG_008951.1:g.35983T>G NG_008951.1:g.35983T>C NG_008951.1:g.35983T>A
ATR transcript variant 1 NM_001184.4:c.3238= NM_001184.4:c.3238T>G NM_001184.4:c.3238T>C NM_001184.4:c.3238T>A
ATR transcript variant 1 NM_001184.3:c.3238= NM_001184.3:c.3238T>G NM_001184.3:c.3238T>C NM_001184.3:c.3238T>A
ATR transcript variant 2 NM_001354579.2:c.3046= NM_001354579.2:c.3046T>G NM_001354579.2:c.3046T>C NM_001354579.2:c.3046T>A
ATR transcript variant 2 NM_001354579.1:c.3046= NM_001354579.1:c.3046T>G NM_001354579.1:c.3046T>C NM_001354579.1:c.3046T>A
ATR transcript variant X1 XM_011512924.2:c.3238= XM_011512924.2:c.3238T>G XM_011512924.2:c.3238T>C XM_011512924.2:c.3238T>A
ATR transcript variant X1 XM_011512924.1:c.3238= XM_011512924.1:c.3238T>G XM_011512924.1:c.3238T>C XM_011512924.1:c.3238T>A
ATR transcript variant X4 XM_011512925.2:c.3046= XM_011512925.2:c.3046T>G XM_011512925.2:c.3046T>C XM_011512925.2:c.3046T>A
ATR transcript variant X4 XM_011512925.1:c.3046= XM_011512925.1:c.3046T>G XM_011512925.1:c.3046T>C XM_011512925.1:c.3046T>A
ATR transcript variant X2 XM_047448360.1:c.3238= XM_047448360.1:c.3238T>G XM_047448360.1:c.3238T>C XM_047448360.1:c.3238T>A
ATR transcript variant X3 XM_047448361.1:c.3238= XM_047448361.1:c.3238T>G XM_047448361.1:c.3238T>C XM_047448361.1:c.3238T>A
ATR transcript variant X6 XM_047448363.1:c.3238= XM_047448363.1:c.3238T>G XM_047448363.1:c.3238T>C XM_047448363.1:c.3238T>A
ATR transcript variant X5 XM_047448362.1:c.3238= XM_047448362.1:c.3238T>G XM_047448362.1:c.3238T>C XM_047448362.1:c.3238T>A
ATR transcript variant X7 XM_047448364.1:c.3238= XM_047448364.1:c.3238T>G XM_047448364.1:c.3238T>C XM_047448364.1:c.3238T>A
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.Leu1080= NP_001175.2:p.Leu1080Val NP_001175.2:p.Leu1080= NP_001175.2:p.Leu1080Met
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.Leu1016= NP_001341508.1:p.Leu1016Val NP_001341508.1:p.Leu1016= NP_001341508.1:p.Leu1016Met
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.Leu1080= XP_011511226.1:p.Leu1080Val XP_011511226.1:p.Leu1080= XP_011511226.1:p.Leu1080Met
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.Leu1016= XP_011511227.1:p.Leu1016Val XP_011511227.1:p.Leu1016= XP_011511227.1:p.Leu1016Met
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.Leu1080= XP_047304316.1:p.Leu1080Val XP_047304316.1:p.Leu1080= XP_047304316.1:p.Leu1080Met
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.Leu1080= XP_047304317.1:p.Leu1080Val XP_047304317.1:p.Leu1080= XP_047304317.1:p.Leu1080Met
serine/threonine-protein kinase ATR isoform X6 XP_047304319.1:p.Leu1080= XP_047304319.1:p.Leu1080Val XP_047304319.1:p.Leu1080= XP_047304319.1:p.Leu1080Met
serine/threonine-protein kinase ATR isoform X5 XP_047304318.1:p.Leu1080= XP_047304318.1:p.Leu1080Val XP_047304318.1:p.Leu1080= XP_047304318.1:p.Leu1080Met
serine/threonine-protein kinase ATR isoform X7 XP_047304320.1:p.Leu1080= XP_047304320.1:p.Leu1080Val XP_047304320.1:p.Leu1080= XP_047304320.1:p.Leu1080Met
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#.

4 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1687243973 Apr 01, 2015 (144)
2 GNOMAD ss2734122344 Nov 08, 2017 (151)
3 TOPMED ss4586378776 Apr 26, 2021 (155)
4 EVA ss5935681506 Oct 12, 2022 (156)
5 ExAC NC_000003.11 - 142266686 Oct 12, 2018 (152)
6 gnomAD - Exomes NC_000003.11 - 142266686 Jul 13, 2019 (153)
7 TopMed NC_000003.12 - 142547844 Apr 26, 2021 (155)
8 ALFA NC_000003.12 - 142547844 Apr 26, 2021 (155)
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
ss5935681506 NC_000003.11:142266685:A:C NC_000003.12:142547843:A:C
7186245, 3211990, ss1687243973, ss2734122344 NC_000003.11:142266685:A:G NC_000003.12:142547843:A:G (self)
423756331, 12827762064, ss4586378776 NC_000003.12:142547843:A:G NC_000003.12:142547843:A:G (self)
ss5935681506 NC_000003.11:142266685:A:T NC_000003.12:142547843:A: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 rs778148931

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