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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.

rs11574156

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:31033642 (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=0.034542 (9143/264690, TOPMED)
T=0.032677 (4573/139944, GnomAD)
T=0.02835 (613/21620, ALFA) (+ 4 more)
T=0.0325 (208/6404, 1000G_30x)
T=0.0308 (154/5008, 1000G)
T=0.019 (4/216, Qatari)
C=0.42 (5/12, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PURG : 2KB Upstream Variant
WRN : 2KB Upstream 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 21620 C=0.97165 T=0.02835
European Sub 14316 C=0.99979 T=0.00021
African Sub 5566 C=0.8956 T=0.1044
African Others Sub 198 C=0.879 T=0.121
African American Sub 5368 C=0.8962 T=0.1038
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.952 T=0.048
Latin American 2 Sub 610 C=0.997 T=0.003
South Asian Sub 98 C=1.00 T=0.00
Other Sub 772 C=0.974 T=0.026


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=0.965458 T=0.034542
gnomAD - Genomes Global Study-wide 139944 C=0.967323 T=0.032677
gnomAD - Genomes European Sub 75842 C=0.99966 T=0.00034
gnomAD - Genomes African Sub 41864 C=0.89688 T=0.10312
gnomAD - Genomes American Sub 13638 C=0.98746 T=0.01254
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.9991 T=0.0009
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2148 C=0.9739 T=0.0261
Allele Frequency Aggregator Total Global 21620 C=0.97165 T=0.02835
Allele Frequency Aggregator European Sub 14316 C=0.99979 T=0.00021
Allele Frequency Aggregator African Sub 5566 C=0.8956 T=0.1044
Allele Frequency Aggregator Other Sub 772 C=0.974 T=0.026
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.997 T=0.003
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.952 T=0.048
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9675 T=0.0325
1000Genomes_30x African Sub 1786 C=0.8886 T=0.1114
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.991 T=0.009
1000Genomes Global Study-wide 5008 C=0.9692 T=0.0308
1000Genomes African Sub 1322 C=0.8880 T=0.1120
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
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=0.991 T=0.009
Qatari Global Study-wide 216 C=0.981 T=0.019
SGDP_PRJ Global Study-wide 12 C=0.42 T=0.58
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.31033642C>T
GRCh37.p13 chr 8 NC_000008.10:g.30891158C>T
WRN RefSeqGene (LRG_524) NG_008870.1:g.5381C>T
Gene: WRN, WRN RecQ like helicase (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
WRN transcript NM_000553.6:c. N/A Upstream Transcript Variant
WRN transcript variant X1 XM_011544639.4:c. N/A Upstream Transcript Variant
WRN transcript variant X5 XM_011544640.2:c. N/A N/A
WRN transcript variant X2 XR_949470.4:n. N/A Upstream Transcript Variant
WRN transcript variant X3 XR_949471.4:n. N/A Upstream Transcript Variant
WRN transcript variant X4 XR_949472.4:n. N/A Upstream Transcript Variant
Gene: PURG, purine rich element binding protein G (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
PURG transcript variant B NM_001015508.3:c. N/A Upstream Transcript Variant
PURG transcript variant C NM_001323311.2:c. N/A Upstream Transcript Variant
PURG transcript variant D NM_001323312.2:c. N/A Upstream Transcript Variant
PURG transcript variant A NM_013357.2:c. N/A Upstream 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: 314044 )
ClinVar Accession Disease Names Clinical Significance
RCV000365374.5 Werner syndrome 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.31033642= NC_000008.11:g.31033642C>T
GRCh37.p13 chr 8 NC_000008.10:g.30891158= NC_000008.10:g.30891158C>T
WRN RefSeqGene (LRG_524) NG_008870.1:g.5381= NG_008870.1:g.5381C>T
WRN transcript NM_000553.4:c.-408= NM_000553.4:c.-408C>T
WRN transcript NM_000553.5:c.-408= NM_000553.5:c.-408C>T
PURG transcript variant B NM_001015508.2:c.-860= NM_001015508.2:c.-860G>A
PURG transcript variant B NM_001015508.1:c.-860= NM_001015508.1:c.-860G>A
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, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss16359298 Feb 28, 2004 (120)
2 1000GENOMES ss223633379 Jul 14, 2010 (132)
3 ILLUMINA ss482088706 May 04, 2012 (137)
4 ILLUMINA ss485604989 May 04, 2012 (137)
5 ILLUMINA ss781645317 Sep 08, 2015 (146)
6 1000GENOMES ss1329254538 Aug 21, 2014 (142)
7 WEILL_CORNELL_DGM ss1928651965 Feb 12, 2016 (147)
8 HUMAN_LONGEVITY ss2301996610 Dec 20, 2016 (150)
9 GNOMAD ss2865043170 Nov 08, 2017 (151)
10 EVA_DECODE ss3721728428 Jul 13, 2019 (153)
11 KHV_HUMAN_GENOMES ss3810986163 Jul 13, 2019 (153)
12 SGDP_PRJ ss3869615311 Apr 26, 2020 (154)
13 TOPMED ss4780946312 Apr 26, 2021 (155)
14 1000G_HIGH_COVERAGE ss5276627805 Oct 16, 2022 (156)
15 EVA ss5380190049 Oct 16, 2022 (156)
16 HUGCELL_USP ss5473251172 Oct 16, 2022 (156)
17 1000G_HIGH_COVERAGE ss5566695340 Oct 16, 2022 (156)
18 SANFORD_IMAGENETICS ss5645093558 Oct 16, 2022 (156)
19 EVA ss5888368010 Oct 16, 2022 (156)
20 EVA ss5974283143 Oct 16, 2022 (156)
21 1000Genomes NC_000008.10 - 30891158 Oct 12, 2018 (152)
22 1000Genomes_30x NC_000008.11 - 31033642 Oct 16, 2022 (156)
23 gnomAD - Genomes NC_000008.11 - 31033642 Apr 26, 2021 (155)
24 Qatari NC_000008.10 - 30891158 Apr 26, 2020 (154)
25 SGDP_PRJ NC_000008.10 - 30891158 Apr 26, 2020 (154)
26 TopMed NC_000008.11 - 31033642 Apr 26, 2021 (155)
27 ALFA NC_000008.11 - 31033642 Apr 26, 2021 (155)
28 ClinVar RCV000365374.5 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss485604989 NC_000008.9:31010699:C:T NC_000008.11:31033641:C:T (self)
41360671, 10693895, 21632291, ss223633379, ss482088706, ss781645317, ss1329254538, ss1928651965, ss2865043170, ss3869615311, ss5380190049, ss5645093558, ss5974283143 NC_000008.10:30891157:C:T NC_000008.11:31033641:C:T (self)
RCV000365374.5, 54221275, 291617586, 618323872, 6618274915, ss2301996610, ss3721728428, ss3810986163, ss4780946312, ss5276627805, ss5473251172, ss5566695340, ss5888368010 NC_000008.11:31033641:C:T NC_000008.11:31033641:C:T (self)
ss16359298 NT_167187.1:18749303:C:T NC_000008.11:31033641: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.

No publications for rs11574156

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