Name: rs368676027
Published: September 21, 2022
License: Open Access

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.

rs368676027

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:142547763 (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>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.000023 (6/264690, TOPMED)
G=0.000016 (4/251256, GnomAD_exome)
G=0.000014 (2/140270, GnomAD) (+ 3 more)
G=0.000016 (2/121228, ExAC)
G=0.00000 (0/14050, ALFA)
G=0.00008 (1/13006, GO-ESP)

Clinical Significance: 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	30370	A=0.99997	G=0.00003
European	Sub	19742	A=0.99995	G=0.00005
African	Sub	7734	A=1.0000	G=0.0000
African Others	Sub	298	A=1.000	G=0.000
African American	Sub	7436	A=1.0000	G=0.0000
Asian	Sub	112	A=1.000	G=0.000
East Asian	Sub	86	A=1.00	G=0.00
Other Asian	Sub	26	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	98	A=1.00	G=0.00
Other	Sub	1928	A=1.0000	G=0.0000

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.999977	G=0.000023
gnomAD - Exomes	Global	Study-wide	251256	A=0.999984	G=0.000016
gnomAD - Exomes	European	Sub	135248	A=0.999978	G=0.000022
gnomAD - Exomes	Asian	Sub	48992	A=0.99998	G=0.00002
gnomAD - Exomes	American	Sub	34558	A=1.00000	G=0.00000
gnomAD - Exomes	African	Sub	16256	A=1.00000	G=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	10076	A=1.00000	G=0.00000
gnomAD - Exomes	Other	Sub	6126	A=1.0000	G=0.0000
gnomAD - Genomes	Global	Study-wide	140270	A=0.999986	G=0.000014
gnomAD - Genomes	European	Sub	75956	A=0.99999	G=0.00001
gnomAD - Genomes	African	Sub	42048	A=1.00000	G=0.00000
gnomAD - Genomes	American	Sub	13658	A=0.99993	G=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=1.0000	G=0.0000
gnomAD - Genomes	East Asian	Sub	3132	A=1.0000	G=0.0000
gnomAD - Genomes	Other	Sub	2154	A=1.0000	G=0.0000
ExAC	Global	Study-wide	121228	A=0.999984	G=0.000016
ExAC	Europe	Sub	73266	A=0.99997	G=0.00003
ExAC	Asian	Sub	25142	A=1.00000	G=0.00000
ExAC	American	Sub	11508	A=1.00000	G=0.00000
ExAC	African	Sub	10406	A=1.00000	G=0.00000
ExAC	Other	Sub	906	A=1.000	G=0.000
Allele Frequency Aggregator	Total	Global	14050	A=1.00000	G=0.00000
Allele Frequency Aggregator	European	Sub	9690	A=1.0000	G=0.0000
Allele Frequency Aggregator	African	Sub	2898	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	496	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	112	A=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	G=0.00
GO Exome Sequencing Project	Global	Study-wide	13006	A=0.99992	G=0.00008
GO Exome Sequencing Project	European American	Sub	8600	A=0.9999	G=0.0001
GO Exome Sequencing Project	African American	Sub	4406	A=1.0000	G=0.0000

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.142547763A>G
GRCh38.p14 chr 3	NC_000003.12:g.142547763A>T
GRCh37.p13 chr 3	NC_000003.11:g.142266605A>G
GRCh37.p13 chr 3	NC_000003.11:g.142266605A>T
ATR RefSeqGene (LRG_1403)	NG_008951.1:g.36064T>C
ATR RefSeqGene (LRG_1403)	NG_008951.1:g.36064T>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.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1	NP_001175.2:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant 1	NM_001184.4:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1	NP_001175.2:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant 2	NM_001354579.2:c.3127T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2	NP_001341508.1:p.Tyr1043H… NP_001341508.1:p.Tyr1043His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant 2	NM_001354579.2:c.3127T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2	NP_001341508.1:p.Tyr1043A… NP_001341508.1:p.Tyr1043Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X1	XM_011512924.2:c.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1	XP_011511226.1:p.Tyr1107H… XP_011511226.1:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X1	XM_011512924.2:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1	XP_011511226.1:p.Tyr1107A… XP_011511226.1:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X2	XM_047448360.1:c.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2	XP_047304316.1:p.Tyr1107H… XP_047304316.1:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X2	XM_047448360.1:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2	XP_047304316.1:p.Tyr1107A… XP_047304316.1:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X3	XM_047448361.1:c.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3	XP_047304317.1:p.Tyr1107H… XP_047304317.1:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X3	XM_047448361.1:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3	XP_047304317.1:p.Tyr1107A… XP_047304317.1:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X4	XM_011512925.2:c.3127T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4	XP_011511227.1:p.Tyr1043H… XP_011511227.1:p.Tyr1043His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X4	XM_011512925.2:c.3127T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4	XP_011511227.1:p.Tyr1043A… XP_011511227.1:p.Tyr1043Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X5	XM_047448362.1:c.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5	XP_047304318.1:p.Tyr1107H… XP_047304318.1:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X5	XM_047448362.1:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X5	XP_047304318.1:p.Tyr1107A… XP_047304318.1:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X6	XM_047448363.1:c.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6	XP_047304319.1:p.Tyr1107H… XP_047304319.1:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X6	XM_047448363.1:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X6	XP_047304319.1:p.Tyr1107A… XP_047304319.1:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant
ATR transcript variant X7	XM_047448364.1:c.3319T>C	Y [TAT] > H [CAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7	XP_047304320.1:p.Tyr1107H… XP_047304320.1:p.Tyr1107His	Y (Tyr) > H (His)	Missense Variant
ATR transcript variant X7	XM_047448364.1:c.3319T>A	Y [TAT] > N [AAT]	Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X7	XP_047304320.1:p.Tyr1107A… XP_047304320.1:p.Tyr1107Asn	Y (Tyr) > N (Asn)	Missense Variant

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: G (allele ID: 1405957 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001981884.3	not provided	Uncertain-Significance

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=	G	T
GRCh38.p14 chr 3	NC_000003.12:g.142547763=	NC_000003.12:g.142547763A>G	NC_000003.12:g.142547763A>T
GRCh37.p13 chr 3	NC_000003.11:g.142266605=	NC_000003.11:g.142266605A>G	NC_000003.11:g.142266605A>T
ATR RefSeqGene (LRG_1403)	NG_008951.1:g.36064=	NG_008951.1:g.36064T>C	NG_008951.1:g.36064T>A
ATR transcript variant 1	NM_001184.4:c.3319=	NM_001184.4:c.3319T>C	NM_001184.4:c.3319T>A
ATR transcript variant 1	NM_001184.3:c.3319=	NM_001184.3:c.3319T>C	NM_001184.3:c.3319T>A
ATR transcript variant 2	NM_001354579.2:c.3127=	NM_001354579.2:c.3127T>C	NM_001354579.2:c.3127T>A
ATR transcript variant 2	NM_001354579.1:c.3127=	NM_001354579.1:c.3127T>C	NM_001354579.1:c.3127T>A
ATR transcript variant X1	XM_011512924.2:c.3319=	XM_011512924.2:c.3319T>C	XM_011512924.2:c.3319T>A
ATR transcript variant X1	XM_011512924.1:c.3319=	XM_011512924.1:c.3319T>C	XM_011512924.1:c.3319T>A
ATR transcript variant X4	XM_011512925.2:c.3127=	XM_011512925.2:c.3127T>C	XM_011512925.2:c.3127T>A
ATR transcript variant X4	XM_011512925.1:c.3127=	XM_011512925.1:c.3127T>C	XM_011512925.1:c.3127T>A
ATR transcript variant X2	XM_047448360.1:c.3319=	XM_047448360.1:c.3319T>C	XM_047448360.1:c.3319T>A
ATR transcript variant X3	XM_047448361.1:c.3319=	XM_047448361.1:c.3319T>C	XM_047448361.1:c.3319T>A
ATR transcript variant X6	XM_047448363.1:c.3319=	XM_047448363.1:c.3319T>C	XM_047448363.1:c.3319T>A
ATR transcript variant X5	XM_047448362.1:c.3319=	XM_047448362.1:c.3319T>C	XM_047448362.1:c.3319T>A
ATR transcript variant X7	XM_047448364.1:c.3319=	XM_047448364.1:c.3319T>C	XM_047448364.1:c.3319T>A
serine/threonine-protein kinase ATR isoform 1	NP_001175.2:p.Tyr1107=	NP_001175.2:p.Tyr1107His	NP_001175.2:p.Tyr1107Asn
serine/threonine-protein kinase ATR isoform 2	NP_001341508.1:p.Tyr1043=	NP_001341508.1:p.Tyr1043His	NP_001341508.1:p.Tyr1043Asn
serine/threonine-protein kinase ATR isoform X1	XP_011511226.1:p.Tyr1107=	XP_011511226.1:p.Tyr1107His	XP_011511226.1:p.Tyr1107Asn
serine/threonine-protein kinase ATR isoform X4	XP_011511227.1:p.Tyr1043=	XP_011511227.1:p.Tyr1043His	XP_011511227.1:p.Tyr1043Asn
serine/threonine-protein kinase ATR isoform X2	XP_047304316.1:p.Tyr1107=	XP_047304316.1:p.Tyr1107His	XP_047304316.1:p.Tyr1107Asn
serine/threonine-protein kinase ATR isoform X3	XP_047304317.1:p.Tyr1107=	XP_047304317.1:p.Tyr1107His	XP_047304317.1:p.Tyr1107Asn
serine/threonine-protein kinase ATR isoform X6	XP_047304319.1:p.Tyr1107=	XP_047304319.1:p.Tyr1107His	XP_047304319.1:p.Tyr1107Asn
serine/threonine-protein kinase ATR isoform X5	XP_047304318.1:p.Tyr1107=	XP_047304318.1:p.Tyr1107His	XP_047304318.1:p.Tyr1107Asn
serine/threonine-protein kinase ATR isoform X7	XP_047304320.1:p.Tyr1107=	XP_047304320.1:p.Tyr1107His	XP_047304320.1:p.Tyr1107Asn

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#.

7 SubSNP, 6 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss712560954	Apr 25, 2013 (138)
2	EVA_EXAC	ss1687243965	Apr 01, 2015 (144)
3	GNOMAD	ss2734122331	Nov 08, 2017 (151)
4	EVA	ss3823963968	Apr 25, 2020 (154)
5	GNOMAD	ss4082178603	Apr 26, 2021 (155)
6	TOPMED	ss4586378759	Apr 26, 2021 (155)
7	EVA	ss5935681432	Oct 12, 2022 (156)
8	ExAC	NC_000003.11 - 142266605	Oct 12, 2018 (152)
9	gnomAD - Genomes	NC_000003.12 - 142547763	Apr 26, 2021 (155)
10	gnomAD - Exomes	NC_000003.11 - 142266605	Jul 13, 2019 (153)
11	GO Exome Sequencing Project	NC_000003.11 - 142266605	Oct 12, 2018 (152)
12	TopMed	NC_000003.12 - 142547763	Apr 26, 2021 (155)
13	ALFA	NC_000003.12 - 142547763	Apr 26, 2021 (155)
14	ClinVar	RCV001981884.3	Oct 12, 2022 (156)

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
7186236, 3211975, 422258, ss712560954, ss1687243965, ss2734122331, ss3823963968, ss5935681432	NC_000003.11:142266604:A:G	NC_000003.12:142547762:A:G	(self)
RCV001981884.3, 126106841, 423756314, 4531621935, ss4082178603, ss4586378759	NC_000003.12:142547762:A:G	NC_000003.12:142547762:A:G	(self)
ss5935681432	NC_000003.11:142266604:A:T	NC_000003.12:142547762:A:T

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

No publications for rs368676027

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs368676027