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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.

rs56030954

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:142466495 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001167 (309/264690, TOPMED)
G=0.000307 (77/250892, GnomAD_exome)
G=0.001126 (158/140280, GnomAD) (+ 6 more)
G=0.000318 (38/119406, ExAC)
G=0.00028 (10/35426, ALFA)
G=0.00108 (14/13006, GO-ESP)
G=0.0003 (2/6404, 1000G_30x)
G=0.0004 (2/5008, 1000G)
G=0.002 (1/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ATR : Synonymous 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 51712 A=0.99948 G=0.00052
European Sub 36630 A=1.00000 G=0.00000
African Sub 7734 A=0.9968 G=0.0032
African Others Sub 296 A=0.993 G=0.007
African American Sub 7438 A=0.9969 G=0.0031
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 500 A=1.000 G=0.000
Latin American 2 Sub 628 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 6010 A=0.9997 G=0.0003


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=0.998833 G=0.001167
gnomAD - Exomes Global Study-wide 250892 A=0.999693 G=0.000307
gnomAD - Exomes European Sub 134962 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48992 A=0.99998 G=0.00002
gnomAD - Exomes American Sub 34516 A=0.99962 G=0.00038
gnomAD - Exomes African Sub 16248 A=0.99618 G=0.00382
gnomAD - Exomes Ashkenazi Jewish Sub 10066 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6108 A=0.9998 G=0.0002
gnomAD - Genomes Global Study-wide 140280 A=0.998874 G=0.001126
gnomAD - Genomes European Sub 75952 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 42064 A=0.99646 G=0.00354
gnomAD - Genomes American Sub 13656 A=0.99934 G=0.00066
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=1.0000 G=0.0000
ExAC Global Study-wide 119406 A=0.999682 G=0.000318
ExAC Europe Sub 72054 A=1.00000 G=0.00000
ExAC Asian Sub 24848 A=1.00000 G=0.00000
ExAC American Sub 11312 A=0.99938 G=0.00062
ExAC African Sub 10298 A=0.99699 G=0.00301
ExAC Other Sub 894 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 35426 A=0.99972 G=0.00028
Allele Frequency Aggregator European Sub 26582 A=1.00000 G=0.00000
Allele Frequency Aggregator Other Sub 4588 A=0.9996 G=0.0004
Allele Frequency Aggregator African Sub 2918 A=0.9973 G=0.0027
Allele Frequency Aggregator Latin American 2 Sub 628 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 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=0.99892 G=0.00108
GO Exome Sequencing Project European American Sub 8600 A=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4406 A=0.9968 G=0.0032
1000Genomes_30x Global Study-wide 6404 A=0.9997 G=0.0003
1000Genomes_30x African Sub 1786 A=0.9989 G=0.0011
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=1.000 G=0.000
1000Genomes Global Study-wide 5008 A=0.9996 G=0.0004
1000Genomes African Sub 1322 A=0.9985 G=0.0015
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=1.000 G=0.000
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.998 G=0.002
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.142466495A>G
GRCh37.p13 chr 3 NC_000003.11:g.142185337A>G
ATR RefSeqGene (LRG_1403) NG_008951.1:g.117332T>C
Gene: ATR, ATR serine/threonine kinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATR transcript variant 1 NM_001184.4:c.6726T>C H [CAT] > H [CAC] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.His2242= H (His) > H (His) Synonymous Variant
ATR transcript variant 2 NM_001354579.2:c.6534T>C H [CAT] > H [CAC] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.His2178= H (His) > H (His) Synonymous Variant
ATR transcript variant X5 XM_047448362.1:c. N/A Genic Downstream Transcript Variant
ATR transcript variant X6 XM_047448363.1:c. N/A Genic Downstream Transcript Variant
ATR transcript variant X7 XM_047448364.1:c. N/A Genic Downstream Transcript Variant
ATR transcript variant X1 XM_011512924.2:c.6732T>C H [CAT] > H [CAC] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.His2244= H (His) > H (His) Synonymous Variant
ATR transcript variant X2 XM_047448360.1:c.6732T>C H [CAT] > H [CAC] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.His2244= H (His) > H (His) Synonymous Variant
ATR transcript variant X3 XM_047448361.1:c.6732T>C H [CAT] > H [CAC] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.His2244= H (His) > H (His) Synonymous Variant
ATR transcript variant X4 XM_011512925.2:c.6540T>C H [CAT] > H [CAC] Coding Sequence Variant
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.His2180= H (His) > H (His) Synonymous 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: G (allele ID: 686345 )
ClinVar Accession Disease Names Clinical Significance
RCV000865096.6 not provided Benign
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= G
GRCh38.p14 chr 3 NC_000003.12:g.142466495= NC_000003.12:g.142466495A>G
GRCh37.p13 chr 3 NC_000003.11:g.142185337= NC_000003.11:g.142185337A>G
ATR RefSeqGene (LRG_1403) NG_008951.1:g.117332= NG_008951.1:g.117332T>C
ATR transcript variant 1 NM_001184.4:c.6726= NM_001184.4:c.6726T>C
ATR transcript variant 1 NM_001184.3:c.6726= NM_001184.3:c.6726T>C
ATR transcript variant 2 NM_001354579.2:c.6534= NM_001354579.2:c.6534T>C
ATR transcript variant 2 NM_001354579.1:c.6534= NM_001354579.1:c.6534T>C
ATR transcript variant X1 XM_011512924.2:c.6732= XM_011512924.2:c.6732T>C
ATR transcript variant X1 XM_011512924.1:c.6732= XM_011512924.1:c.6732T>C
ATR transcript variant X4 XM_011512925.2:c.6540= XM_011512925.2:c.6540T>C
ATR transcript variant X4 XM_011512925.1:c.6540= XM_011512925.1:c.6540T>C
ATR transcript variant X2 XM_047448360.1:c.6732= XM_047448360.1:c.6732T>C
ATR transcript variant X3 XM_047448361.1:c.6732= XM_047448361.1:c.6732T>C
serine/threonine-protein kinase ATR isoform 1 NP_001175.2:p.His2242= NP_001175.2:p.His2242=
serine/threonine-protein kinase ATR isoform 2 NP_001341508.1:p.His2178= NP_001341508.1:p.His2178=
serine/threonine-protein kinase ATR isoform X1 XP_011511226.1:p.His2244= XP_011511226.1:p.His2244=
serine/threonine-protein kinase ATR isoform X4 XP_011511227.1:p.His2180= XP_011511227.1:p.His2180=
serine/threonine-protein kinase ATR isoform X2 XP_047304316.1:p.His2244= XP_047304316.1:p.His2244=
serine/threonine-protein kinase ATR isoform X3 XP_047304317.1:p.His2244= XP_047304317.1:p.His2244=
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#.

20 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CANCER-GENOME ss74801355 Dec 07, 2007 (129)
2 NHLBI-ESP ss342149213 May 09, 2011 (134)
3 1000GENOMES ss456574248 Sep 17, 2011 (135)
4 1000GENOMES ss490875406 May 04, 2012 (137)
5 1000GENOMES ss1306471138 Aug 21, 2014 (142)
6 EVA_EXAC ss1687243176 Apr 01, 2015 (144)
7 EVA_MGP ss1711037027 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2256473889 Dec 20, 2016 (150)
9 GNOMAD ss2734121145 Nov 08, 2017 (151)
10 GNOMAD ss2747116424 Nov 08, 2017 (151)
11 GNOMAD ss2800027713 Nov 08, 2017 (151)
12 EVA ss3823963794 Apr 25, 2020 (154)
13 TOPMED ss4586360606 Apr 27, 2021 (155)
14 1000G_HIGH_COVERAGE ss5256298864 Oct 12, 2022 (156)
15 EVA ss5343771552 Oct 12, 2022 (156)
16 HUGCELL_USP ss5455409506 Oct 12, 2022 (156)
17 1000G_HIGH_COVERAGE ss5535879540 Oct 12, 2022 (156)
18 SANFORD_IMAGENETICS ss5633342366 Oct 12, 2022 (156)
19 EVA ss5871316124 Oct 12, 2022 (156)
20 EVA ss5961699364 Oct 12, 2022 (156)
21 1000Genomes NC_000003.11 - 142185337 Oct 12, 2018 (152)
22 1000Genomes_30x NC_000003.12 - 142466495 Oct 12, 2022 (156)
23 ExAC NC_000003.11 - 142185337 Oct 12, 2018 (152)
24 gnomAD - Genomes NC_000003.12 - 142466495 Apr 27, 2021 (155)
25 gnomAD - Exomes NC_000003.11 - 142185337 Jul 13, 2019 (153)
26 GO Exome Sequencing Project NC_000003.11 - 142185337 Oct 12, 2018 (152)
27 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 142185337 Apr 25, 2020 (154)
28 TopMed NC_000003.12 - 142466495 Apr 27, 2021 (155)
29 ALFA NC_000003.12 - 142466495 Apr 27, 2021 (155)
30 ClinVar RCV000865096.6 Oct 12, 2022 (156)
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
17745058, 7185319, 3210715, 422083, 152787, ss342149213, ss456574248, ss490875406, ss1306471138, ss1687243176, ss1711037027, ss2734121145, ss2747116424, ss2800027713, ss3823963794, ss5343771552, ss5633342366, ss5961699364 NC_000003.11:142185336:A:G NC_000003.12:142466494:A:G (self)
RCV000865096.6, 23405475, 126091307, 423738161, 6331757028, ss2256473889, ss4586360606, ss5256298864, ss5455409506, ss5535879540, ss5871316124 NC_000003.12:142466494:A:G NC_000003.12:142466494:A:G (self)
ss74801355 NT_005612.16:48680482:A:G NC_000003.12:142466494:A:G (self)
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 rs56030954

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