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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.

rs3087425

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:31120294 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.001708 (452/264690, TOPMED)
T=0.002835 (712/251178, GnomAD_exome)
T=0.001052 (153/145502, ALFA) (+ 7 more)
T=0.000886 (124/139954, GnomAD)
T=0.002085 (253/121368, ExAC)
T=0.00384 (302/78696, PAGE_STUDY)
T=0.0019 (12/6404, 1000G_30x)
T=0.0018 (9/5008, 1000G)
T=0.0109 (13/1194, HapMap)
C=0.4 (3/8, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
WRN : Missense Variant
Publications
4 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 161848 C=0.999030 T=0.000970
European Sub 131988 C=0.999909 T=0.000091
African Sub 12466 C=0.99984 T=0.00016
African Others Sub 430 C=1.000 T=0.000
African American Sub 12036 C=0.99983 T=0.00017
Asian Sub 710 C=1.000 T=0.000
East Asian Sub 548 C=1.000 T=0.000
Other Asian Sub 162 C=1.000 T=0.000
Latin American 1 Sub 734 C=1.000 T=0.000
Latin American 2 Sub 6244 C=0.9801 T=0.0199
South Asian Sub 190 C=1.000 T=0.000
Other Sub 9516 C=0.9980 T=0.0020


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 C=0.998292 T=0.001708
gnomAD - Exomes Global Study-wide 251178 C=0.997165 T=0.002835
gnomAD - Exomes European Sub 135156 C=0.999956 T=0.000044
gnomAD - Exomes Asian Sub 48998 C=0.99973 T=0.00027
gnomAD - Exomes American Sub 34584 C=0.98025 T=0.01975
gnomAD - Exomes African Sub 16248 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6124 C=0.9985 T=0.0015
Allele Frequency Aggregator Total Global 145502 C=0.998948 T=0.001052
Allele Frequency Aggregator European Sub 121908 C=0.999918 T=0.000082
Allele Frequency Aggregator Other Sub 8082 C=0.9978 T=0.0022
Allele Frequency Aggregator African Sub 7634 C=0.9999 T=0.0001
Allele Frequency Aggregator Latin American 2 Sub 6244 C=0.9801 T=0.0199
Allele Frequency Aggregator Latin American 1 Sub 734 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 710 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 190 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 139954 C=0.999114 T=0.000886
gnomAD - Genomes European Sub 75794 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 41966 C=0.99955 T=0.00045
gnomAD - Genomes American Sub 13594 C=0.99264 T=0.00736
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 C=0.9997 T=0.0003
gnomAD - Genomes Other Sub 2152 C=0.9991 T=0.0009
ExAC Global Study-wide 121368 C=0.997915 T=0.002085
ExAC Europe Sub 73330 C=0.99997 T=0.00003
ExAC Asian Sub 25156 C=0.99972 T=0.00028
ExAC American Sub 11570 C=0.97891 T=0.02109
ExAC African Sub 10404 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
The PAGE Study Global Study-wide 78696 C=0.99616 T=0.00384
The PAGE Study AfricanAmerican Sub 32512 C=0.99963 T=0.00037
The PAGE Study Mexican Sub 10810 C=0.98085 T=0.01915
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7916 C=0.9985 T=0.0015
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=0.9981 T=0.0019
The PAGE Study Dominican Sub 3828 C=0.9995 T=0.0005
The PAGE Study CentralAmerican Sub 2450 C=0.9845 T=0.0155
The PAGE Study SouthAmerican Sub 1982 C=0.9919 T=0.0081
The PAGE Study NativeAmerican Sub 1260 C=0.9944 T=0.0056
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
1000Genomes_30x Global Study-wide 6404 C=0.9981 T=0.0019
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9992 T=0.0008
1000Genomes_30x East Asian Sub 1170 C=0.9983 T=0.0017
1000Genomes_30x American Sub 980 C=0.991 T=0.009
1000Genomes Global Study-wide 5008 C=0.9982 T=0.0018
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9980 T=0.0020
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=0.990 T=0.010
HapMap Global Study-wide 1194 C=0.9891 T=0.0109
HapMap American Sub 556 C=0.986 T=0.014
HapMap African Sub 298 C=0.997 T=0.003
HapMap Asian Sub 170 C=0.988 T=0.012
HapMap Europe Sub 170 C=0.988 T=0.012
SGDP_PRJ Global Study-wide 8 C=0.4 T=0.6
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 8 NC_000008.11:g.31120294C>T
GRCh37.p13 chr 8 NC_000008.10:g.30977810C>T
WRN RefSeqGene (LRG_524) NG_008870.1:g.92033C>T
Gene: WRN, WRN RecQ like helicase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
WRN transcript NM_000553.6:c.2500C>T R [CGC] > C [TGC] Coding Sequence Variant
bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN NP_000544.2:p.Arg834Cys R (Arg) > C (Cys) Missense Variant
WRN transcript variant X1 XM_011544639.4:c.2419C>T R [CGC] > C [TGC] Coding Sequence Variant
bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN isoform X1 XP_011542941.1:p.Arg807Cys R (Arg) > C (Cys) Missense Variant
WRN transcript variant X5 XM_011544640.2:c.901C>T R [CGC] > C [TGC] Coding Sequence Variant
bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN isoform X2 XP_011542942.1:p.Arg301Cys R (Arg) > C (Cys) Missense Variant
WRN transcript variant X2 XR_949470.4:n.2740C>T N/A Non Coding Transcript Variant
WRN transcript variant X3 XR_949471.4:n.2740C>T N/A Non Coding Transcript Variant
WRN transcript variant X4 XR_949472.4:n.2740C>T N/A Non Coding Transcript 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: 47491 )
ClinVar Accession Disease Names Clinical Significance
RCV000032137.12 Werner syndrome Benign-Likely-Benign
RCV000122280.5 not specified Benign-Likely-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 C= T
GRCh38.p14 chr 8 NC_000008.11:g.31120294= NC_000008.11:g.31120294C>T
GRCh37.p13 chr 8 NC_000008.10:g.30977810= NC_000008.10:g.30977810C>T
WRN RefSeqGene (LRG_524) NG_008870.1:g.92033= NG_008870.1:g.92033C>T
WRN transcript NM_000553.6:c.2500= NM_000553.6:c.2500C>T
WRN transcript NM_000553.5:c.2500= NM_000553.5:c.2500C>T
WRN transcript NM_000553.4:c.2500= NM_000553.4:c.2500C>T
WRN transcript variant X1 XM_011544639.4:c.2419= XM_011544639.4:c.2419C>T
WRN transcript variant X1 XM_011544639.3:c.2419= XM_011544639.3:c.2419C>T
WRN transcript variant X1 XM_011544639.2:c.2419= XM_011544639.2:c.2419C>T
WRN transcript variant X1 XM_011544639.1:c.2419= XM_011544639.1:c.2419C>T
WRN transcript variant X3 XR_949471.4:n.2740= XR_949471.4:n.2740C>T
WRN transcript variant X4 XR_949471.3:n.2801= XR_949471.3:n.2801C>T
WRN transcript variant X3 XR_949471.2:n.2770= XR_949471.2:n.2770C>T
WRN transcript variant X3 XR_949471.1:n.2773= XR_949471.1:n.2773C>T
WRN transcript variant X4 XR_949472.4:n.2740= XR_949472.4:n.2740C>T
WRN transcript variant X5 XR_949472.3:n.2801= XR_949472.3:n.2801C>T
WRN transcript variant X4 XR_949472.2:n.2770= XR_949472.2:n.2770C>T
WRN transcript variant X4 XR_949472.1:n.2773= XR_949472.1:n.2773C>T
WRN transcript variant X2 XR_949470.4:n.2740= XR_949470.4:n.2740C>T
WRN transcript variant X3 XR_949470.3:n.2801= XR_949470.3:n.2801C>T
WRN transcript variant X2 XR_949470.2:n.2770= XR_949470.2:n.2770C>T
WRN transcript variant X2 XR_949470.1:n.2773= XR_949470.1:n.2773C>T
WRN transcript variant X5 XM_011544640.2:c.901= XM_011544640.2:c.901C>T
WRN transcript variant X6 XM_011544640.1:c.901= XM_011544640.1:c.901C>T
bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN NP_000544.2:p.Arg834= NP_000544.2:p.Arg834Cys
bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN isoform X1 XP_011542941.1:p.Arg807= XP_011542941.1:p.Arg807Cys
bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN isoform X2 XP_011542942.1:p.Arg301= XP_011542942.1:p.Arg301Cys
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#.

67 SubSNP, 10 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 UWGC ss4318975 Jan 05, 2002 (102)
2 SNP500CANCER ss5586964 Mar 31, 2003 (113)
3 EGP_SNPS ss16359516 Feb 27, 2004 (120)
4 AFFY ss74820096 Aug 16, 2007 (128)
5 ILLUMINA ss74909516 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss119453575 Dec 01, 2009 (131)
7 ILLUMINA ss160608752 Dec 01, 2009 (131)
8 ILLUMINA ss173557778 Jul 04, 2010 (132)
9 ILLUMINA ss244293538 Jul 04, 2010 (132)
10 1000GENOMES ss334789506 May 09, 2011 (134)
11 ILLUMINA ss480747272 May 04, 2012 (137)
12 ILLUMINA ss480763155 May 04, 2012 (137)
13 ILLUMINA ss481649407 Sep 08, 2015 (146)
14 ILLUMINA ss485168416 May 04, 2012 (137)
15 1000GENOMES ss490963330 May 04, 2012 (137)
16 EXOME_CHIP ss491412312 May 04, 2012 (137)
17 ILLUMINA ss537159758 Sep 08, 2015 (146)
18 GENEREVIEWS ss550898337 Nov 14, 2012 (137)
19 ILLUMINA ss778515286 Sep 08, 2015 (146)
20 ILLUMINA ss783030418 Sep 08, 2015 (146)
21 ILLUMINA ss783990121 Sep 08, 2015 (146)
22 ILLUMINA ss832288035 Sep 08, 2015 (146)
23 ILLUMINA ss833971599 Sep 08, 2015 (146)
24 1000GENOMES ss1329256770 Aug 21, 2014 (142)
25 EVA_EXAC ss1689157502 Apr 01, 2015 (144)
26 ILLUMINA ss1752728793 Sep 08, 2015 (146)
27 ILLUMINA ss1959101948 Feb 12, 2016 (147)
28 HUMAN_LONGEVITY ss2302001221 Dec 20, 2016 (150)
29 ILLUMINA ss2634732863 Nov 08, 2017 (151)
30 GNOMAD ss2737093573 Nov 08, 2017 (151)
31 GNOMAD ss2748029799 Nov 08, 2017 (151)
32 GNOMAD ss2865049610 Nov 08, 2017 (151)
33 AFFY ss2985435938 Nov 08, 2017 (151)
34 ILLUMINA ss3022835023 Nov 08, 2017 (151)
35 ILLUMINA ss3630034294 Oct 12, 2018 (152)
36 ILLUMINA ss3632632733 Oct 12, 2018 (152)
37 ILLUMINA ss3633497142 Oct 12, 2018 (152)
38 ILLUMINA ss3634223760 Oct 12, 2018 (152)
39 ILLUMINA ss3635166947 Oct 12, 2018 (152)
40 ILLUMINA ss3635902638 Oct 12, 2018 (152)
41 ILLUMINA ss3636904093 Oct 12, 2018 (152)
42 ILLUMINA ss3637655795 Oct 12, 2018 (152)
43 ILLUMINA ss3638753579 Oct 12, 2018 (152)
44 ILLUMINA ss3640874237 Oct 12, 2018 (152)
45 ILLUMINA ss3643684963 Oct 12, 2018 (152)
46 ILLUMINA ss3653376407 Oct 12, 2018 (152)
47 ILLUMINA ss3654197958 Oct 12, 2018 (152)
48 ILLUMINA ss3726528362 Jul 13, 2019 (153)
49 ILLUMINA ss3745466760 Jul 13, 2019 (153)
50 EVA ss3767825820 Jul 13, 2019 (153)
51 PAGE_CC ss3771435152 Jul 13, 2019 (153)
52 ILLUMINA ss3772959280 Jul 13, 2019 (153)
53 SGDP_PRJ ss3869616382 Apr 26, 2020 (154)
54 EVA ss4017384577 Apr 26, 2021 (155)
55 TOPMED ss4780966317 Apr 26, 2021 (155)
56 EVA ss5237439907 Apr 26, 2021 (155)
57 1000G_HIGH_COVERAGE ss5276629673 Oct 16, 2022 (156)
58 EVA ss5380193559 Oct 16, 2022 (156)
59 HUGCELL_USP ss5473252889 Oct 16, 2022 (156)
60 1000G_HIGH_COVERAGE ss5566698235 Oct 16, 2022 (156)
61 SANFORD_IMAGENETICS ss5624690681 Oct 16, 2022 (156)
62 SANFORD_IMAGENETICS ss5645094547 Oct 16, 2022 (156)
63 EVA ss5848173035 Oct 16, 2022 (156)
64 EVA ss5888370289 Oct 16, 2022 (156)
65 EVA ss5935923623 Oct 16, 2022 (156)
66 EVA ss5974284312 Oct 16, 2022 (156)
67 EVA ss5979859591 Oct 16, 2022 (156)
68 1000Genomes NC_000008.10 - 30977810 Oct 12, 2018 (152)
69 1000Genomes_30x NC_000008.11 - 31120294 Oct 16, 2022 (156)
70 ExAC NC_000008.10 - 30977810 Oct 12, 2018 (152)
71 gnomAD - Genomes NC_000008.11 - 31120294 Apr 26, 2021 (155)
72 gnomAD - Exomes NC_000008.10 - 30977810 Jul 13, 2019 (153)
73 HapMap NC_000008.11 - 31120294 Apr 26, 2020 (154)
74 The PAGE Study NC_000008.11 - 31120294 Jul 13, 2019 (153)
75 SGDP_PRJ NC_000008.10 - 30977810 Apr 26, 2020 (154)
76 TopMed NC_000008.11 - 31120294 Apr 26, 2021 (155)
77 ALFA NC_000008.11 - 31120294 Apr 26, 2021 (155)
78 ClinVar RCV000032137.12 Oct 16, 2022 (156)
79 ClinVar RCV000122280.5 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)
rs52836442 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss480747272, ss3643684963 NC_000008.9:31097351:C:T NC_000008.11:31120293:C:T (self)
41363001, 9254470, 6264093, 21633362, ss334789506, ss480763155, ss481649407, ss485168416, ss490963330, ss491412312, ss537159758, ss778515286, ss783030418, ss783990121, ss832288035, ss833971599, ss1329256770, ss1689157502, ss1752728793, ss1959101948, ss2634732863, ss2737093573, ss2748029799, ss2865049610, ss2985435938, ss3022835023, ss3630034294, ss3632632733, ss3633497142, ss3634223760, ss3635166947, ss3635902638, ss3636904093, ss3637655795, ss3638753579, ss3640874237, ss3653376407, ss3654197958, ss3745466760, ss3767825820, ss3772959280, ss3869616382, ss4017384577, ss5237439907, ss5380193559, ss5624690681, ss5645094547, ss5848173035, ss5935923623, ss5974284312, ss5979859591 NC_000008.10:30977809:C:T NC_000008.11:31120293:C:T (self)
RCV000032137.12, RCV000122280.5, 54224170, 291633791, 3598550, 656621, 618343877, 3782834664, ss550898337, ss2302001221, ss3726528362, ss3771435152, ss4780966317, ss5276629673, ss5473252889, ss5566698235, ss5888370289 NC_000008.11:31120293:C:T NC_000008.11:31120293:C:T (self)
ss4318975, ss5586964, ss16359516, ss74820096, ss74909516, ss119453575, ss160608752, ss173557778, ss244293538 NT_167187.1:18835955:C:T NC_000008.11:31120293:C:T (self)
Help

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

4 citations for rs3087425
PMID Title Author Year Journal
15489508 The enzymatic activities of the Werner syndrome protein are disabled by the amino acid polymorphism R834C. Kamath-Loeb AS et al. 2004 The Journal of biological chemistry
20301687 Werner Syndrome. Oshima J et al. 1993 GeneReviews(®)
24728327 Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL et al. 2014 PloS one
28276523 Homozygosity for the WRN Helicase-Inactivating Variant, R834C, does not confer a Werner syndrome clinical phenotype. Kamath-Loeb AS et al. 2017 Scientific reports
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