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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.

rs45499692

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:129752993 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.007050 (1866/264690, TOPMED)
T=0.001649 (404/245070, GnomAD_exome)
T=0.007028 (986/140290, GnomAD) (+ 8 more)
T=0.002069 (244/117950, ExAC)
T=0.00119 (106/88912, ALFA)
T=0.01061 (834/78626, PAGE_STUDY)
T=0.00777 (101/13006, GO-ESP)
T=0.0059 (38/6404, 1000G_30x)
T=0.0062 (31/5008, 1000G)
T=0.0005 (2/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTGES : 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 88912 A=0.99881 T=0.00119
European Sub 75636 A=0.99991 T=0.00009
African Sub 4354 A=0.9798 T=0.0202
African Others Sub 174 A=0.960 T=0.040
African American Sub 4180 A=0.9806 T=0.0194
Asian Sub 3330 A=1.0000 T=0.0000
East Asian Sub 2674 A=1.0000 T=0.0000
Other Asian Sub 656 A=1.000 T=0.000
Latin American 1 Sub 436 A=0.991 T=0.009
Latin American 2 Sub 928 A=0.999 T=0.001
South Asian Sub 274 A=1.000 T=0.000
Other Sub 3954 A=0.9985 T=0.0015


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=0.992950 T=0.007050
gnomAD - Exomes Global Study-wide 245070 A=0.998351 T=0.001649
gnomAD - Exomes European Sub 129372 A=0.999923 T=0.000077
gnomAD - Exomes Asian Sub 48918 A=1.00000 T=0.00000
gnomAD - Exomes American Sub 34516 A=0.99913 T=0.00087
gnomAD - Exomes African Sub 16164 A=0.97779 T=0.02221
gnomAD - Exomes Ashkenazi Jewish Sub 10026 A=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6074 A=0.9992 T=0.0008
gnomAD - Genomes Global Study-wide 140290 A=0.992972 T=0.007028
gnomAD - Genomes European Sub 75966 A=0.99987 T=0.00013
gnomAD - Genomes African Sub 42050 A=0.97772 T=0.02228
gnomAD - Genomes American Sub 13666 A=0.99780 T=0.00220
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9958 T=0.0042
ExAC Global Study-wide 117950 A=0.997931 T=0.002069
ExAC Europe Sub 71000 A=0.99990 T=0.00010
ExAC Asian Sub 24628 A=1.00000 T=0.00000
ExAC American Sub 11400 A=0.99939 T=0.00061
ExAC African Sub 10052 A=0.97712 T=0.02288
ExAC Other Sub 870 A=1.000 T=0.000
Allele Frequency Aggregator Total Global 88912 A=0.99881 T=0.00119
Allele Frequency Aggregator European Sub 75636 A=0.99991 T=0.00009
Allele Frequency Aggregator African Sub 4354 A=0.9798 T=0.0202
Allele Frequency Aggregator Other Sub 3954 A=0.9985 T=0.0015
Allele Frequency Aggregator Asian Sub 3330 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 928 A=0.999 T=0.001
Allele Frequency Aggregator Latin American 1 Sub 436 A=0.991 T=0.009
Allele Frequency Aggregator South Asian Sub 274 A=1.000 T=0.000
The PAGE Study Global Study-wide 78626 A=0.98939 T=0.01061
The PAGE Study AfricanAmerican Sub 32452 A=0.97837 T=0.02163
The PAGE Study Mexican Sub 10806 A=0.99926 T=0.00074
The PAGE Study Asian Sub 8318 A=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 A=0.9933 T=0.0067
The PAGE Study NativeHawaiian Sub 4534 A=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 A=0.9962 T=0.0038
The PAGE Study Dominican Sub 3824 A=0.9903 T=0.0097
The PAGE Study CentralAmerican Sub 2446 A=0.9971 T=0.0029
The PAGE Study SouthAmerican Sub 1982 A=0.9975 T=0.0025
The PAGE Study NativeAmerican Sub 1260 A=0.9952 T=0.0048
The PAGE Study SouthAsian Sub 856 A=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 A=0.99223 T=0.00777
GO Exome Sequencing Project European American Sub 8600 A=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 A=0.9771 T=0.0229
1000Genomes_30x Global Study-wide 6404 A=0.9941 T=0.0059
1000Genomes_30x African Sub 1786 A=0.9798 T=0.0202
1000Genomes_30x Europe Sub 1266 A=0.9992 T=0.0008
1000Genomes_30x South Asian Sub 1202 A=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 T=0.0000
1000Genomes_30x American Sub 980 A=0.999 T=0.001
1000Genomes Global Study-wide 5008 A=0.9938 T=0.0062
1000Genomes African Sub 1322 A=0.9781 T=0.0219
1000Genomes East Asian Sub 1008 A=1.0000 T=0.0000
1000Genomes Europe Sub 1006 A=0.9990 T=0.0010
1000Genomes South Asian Sub 978 A=1.000 T=0.000
1000Genomes American Sub 694 A=0.999 T=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9995 T=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.0000 T=0.0000
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 9 NC_000009.12:g.129752993A>T
GRCh37.p13 chr 9 NC_000009.11:g.132515272A>T
Gene: PTGES, prostaglandin E synthase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTGES transcript NM_004878.5:c.20T>A V [GTG] > E [GAG] Coding Sequence Variant
prostaglandin E synthase NP_004869.1:p.Val7Glu V (Val) > E (Glu) 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: 723359 )
ClinVar Accession Disease Names Clinical Significance
RCV000892616.3 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= T
GRCh38.p14 chr 9 NC_000009.12:g.129752993= NC_000009.12:g.129752993A>T
GRCh37.p13 chr 9 NC_000009.11:g.132515272= NC_000009.11:g.132515272A>T
PTGES transcript NM_004878.5:c.20= NM_004878.5:c.20T>A
PTGES transcript NM_004878.4:c.20= NM_004878.4:c.20T>A
PTGES transcript variant 2 NM_198797.1:c.20= NM_198797.1:c.20T>A
prostaglandin E synthase NP_004869.1:p.Val7= NP_004869.1:p.Val7Glu
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#.

45 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss70354370 May 17, 2007 (127)
2 CORNELL ss86244717 Mar 23, 2008 (130)
3 CANCER-GENOME ss86344262 Mar 23, 2008 (130)
4 1000GENOMES ss224475658 Jul 14, 2010 (132)
5 NHLBI-ESP ss342285968 May 09, 2011 (134)
6 1000GENOMES ss490987235 May 04, 2012 (137)
7 GSK-GENETICS ss491280972 May 04, 2012 (137)
8 EXOME_CHIP ss491429003 May 04, 2012 (137)
9 ILLUMINA ss780881692 Aug 21, 2014 (142)
10 ILLUMINA ss783567431 Aug 21, 2014 (142)
11 1000GENOMES ss1335629611 Aug 21, 2014 (142)
12 EVA_UK10K_ALSPAC ss1623657735 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1666651768 Apr 01, 2015 (144)
14 EVA_EXAC ss1689693270 Apr 01, 2015 (144)
15 ILLUMINA ss1752762343 Sep 08, 2015 (146)
16 ILLUMINA ss1917841696 Feb 12, 2016 (147)
17 ILLUMINA ss1946270403 Feb 12, 2016 (147)
18 ILLUMINA ss1959220407 Feb 12, 2016 (147)
19 HUMAN_LONGEVITY ss2314799616 Dec 20, 2016 (150)
20 GNOMAD ss2737925964 Nov 08, 2017 (151)
21 GNOMAD ss2748284296 Nov 08, 2017 (151)
22 GNOMAD ss2883717003 Nov 08, 2017 (151)
23 ILLUMINA ss3022969577 Nov 08, 2017 (151)
24 ILLUMINA ss3630366772 Oct 12, 2018 (152)
25 ILLUMINA ss3635235379 Oct 12, 2018 (152)
26 ILLUMINA ss3640942668 Oct 12, 2018 (152)
27 ILLUMINA ss3645003742 Oct 12, 2018 (152)
28 ILLUMINA ss3653525976 Oct 12, 2018 (152)
29 EVA_DECODE ss3724839491 Jul 13, 2019 (153)
30 ILLUMINA ss3726647433 Jul 13, 2019 (153)
31 ILLUMINA ss3744594542 Jul 13, 2019 (153)
32 ILLUMINA ss3745535286 Jul 13, 2019 (153)
33 PAGE_CC ss3771528479 Jul 13, 2019 (153)
34 ILLUMINA ss3773027081 Jul 13, 2019 (153)
35 EVA ss3824473616 Apr 26, 2020 (154)
36 EVA ss3986464314 Apr 26, 2021 (155)
37 TOPMED ss4837199659 Apr 26, 2021 (155)
38 1000G_HIGH_COVERAGE ss5282331533 Oct 16, 2022 (156)
39 EVA ss5390541337 Oct 16, 2022 (156)
40 HUGCELL_USP ss5478184373 Oct 16, 2022 (156)
41 1000G_HIGH_COVERAGE ss5575466490 Oct 16, 2022 (156)
42 SANFORD_IMAGENETICS ss5648348581 Oct 16, 2022 (156)
43 EVA ss5848221233 Oct 16, 2022 (156)
44 EVA ss5918201952 Oct 16, 2022 (156)
45 EVA ss5977562637 Oct 16, 2022 (156)
46 1000Genomes NC_000009.11 - 132515272 Oct 12, 2018 (152)
47 1000Genomes_30x NC_000009.12 - 129752993 Oct 16, 2022 (156)
48 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 132515272 Oct 12, 2018 (152)
49 ExAC NC_000009.11 - 132515272 Oct 12, 2018 (152)
50 gnomAD - Genomes NC_000009.12 - 129752993 Apr 26, 2021 (155)
51 gnomAD - Exomes NC_000009.11 - 132515272 Jul 13, 2019 (153)
52 GO Exome Sequencing Project NC_000009.11 - 132515272 Oct 12, 2018 (152)
53 The PAGE Study NC_000009.12 - 129752993 Jul 13, 2019 (153)
54 TopMed NC_000009.12 - 129752993 Apr 26, 2021 (155)
55 UK 10K study - Twins NC_000009.11 - 132515272 Oct 12, 2018 (152)
56 ALFA NC_000009.12 - 129752993 Apr 26, 2021 (155)
57 ClinVar RCV000892616.3 Oct 16, 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).

Associated ID History Updated (Build)
rs61737989 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491280972 NC_000009.10:131555092:A:T NC_000009.12:129752992:A:T (self)
47953907, 26653058, 9831749, 7114930, 931366, 26653058, ss224475658, ss342285968, ss490987235, ss491429003, ss780881692, ss783567431, ss1335629611, ss1623657735, ss1666651768, ss1689693270, ss1752762343, ss1917841696, ss1946270403, ss1959220407, ss2737925964, ss2748284296, ss2883717003, ss3022969577, ss3630366772, ss3635235379, ss3640942668, ss3645003742, ss3653525976, ss3744594542, ss3745535286, ss3773027081, ss3824473616, ss3986464314, ss5390541337, ss5648348581, ss5848221233, ss5977562637 NC_000009.11:132515271:A:T NC_000009.12:129752992:A:T (self)
RCV000892616.3, 62992425, 338933840, 749948, 674577220, 4756506850, ss2314799616, ss3724839491, ss3726647433, ss3771528479, ss4837199659, ss5282331533, ss5478184373, ss5575466490, ss5918201952 NC_000009.12:129752992:A:T NC_000009.12:129752992:A:T (self)
ss70354370, ss86244717, ss86344262 NT_008470.19:61679803:A:T NC_000009.12:129752992:A:T (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 rs45499692

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