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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.

rs11202592

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87864461 (GRCh38.p12) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.003821 (961/251482, GnomAD_exome)
G=0.004404 (553/125568, TOPMED)
G=0.003624 (440/121404, ExAC) (+ 12 more)
G=0.00331 (104/31402, GnomAD)
G=0.00015 (2/13006, GO-ESP)
G=0.00027 (3/11176, ALFA Project)
G=0.0110 (55/5008, 1000G)
G=0.0002 (1/4480, Estonian)
G=0.0003 (1/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
G=0.0407 (119/2922, KOREAN)
G=0.0251 (46/1832, Korea1K)
G=0.073 (45/613, Vietnamese)
C=0.50 (7/14, SGDP_PRJ)
G=0.50 (7/14, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Missense Variant
KLLN : 2KB Upstream Variant
Publications
6 citations
Genomic View
See rs on genome
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.p12 chr 10 NC_000010.11:g.87864461C>G
GRCh37.p13 chr 10 NC_000010.10:g.89624218C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.6023C>G
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.3977G>C
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.80284C>G
Gene: PTEN, phosphatase and tensin homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 2 NM_001304718.2:c.-714= N/A 5 Prime UTR Variant
PTEN transcript variant 1 NM_000314.8:c.-9= N/A 5 Prime UTR Variant
PTEN transcript variant 1 NM_001304717.5:c.511C>G L [CTC] > V [GTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Leu171Val L (Leu) > V (Val) Missense Variant
Gene: KLLN, killin, p53 regulated DNA replication inhibitor (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
KLLN transcript NM_001126049.1: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: G (allele ID: 98715 )
ClinVar Accession Disease Names Clinical Significance
RCV000078600.6 not specified Benign
RCV000131696.2 Hereditary cancer-predisposing syndrome Benign
RCV000203697.3 PTEN hamartoma tumor syndrome Benign
RCV000409463.1 Cowden syndrome 1 Benign

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 49260 C=0.99980 G=0.00020
European Sub 37246 C=0.99992 G=0.00008
African Sub 3560 C=1.0000 G=0.0000
African Others Sub 122 C=1.000 G=0.000
African American Sub 3438 C=1.0000 G=0.0000
Asian Sub 168 C=0.976 G=0.024
East Asian Sub 112 C=0.973 G=0.027
Other Asian Sub 56 C=0.98 G=0.02
Latin American 1 Sub 500 C=1.000 G=0.000
Latin American 2 Sub 628 C=1.000 G=0.000
South Asian Sub 98 C=0.99 G=0.01
Other Sub 7060 C=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
gnomAD - Exomes Global Study-wide 251482 C=0.996179 G=0.003821
gnomAD - Exomes European Sub 135408 C=0.999897 G=0.000103
gnomAD - Exomes Asian Sub 49010 C=0.98088 G=0.01912
gnomAD - Exomes American Sub 34592 C=0.99997 G=0.00003
gnomAD - Exomes African Sub 16254 C=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6138 C=0.9985 G=0.0015
TopMed Global Study-wide 125568 C=0.995596 G=0.004404
ExAC Global Study-wide 121404 C=0.996376 G=0.003624
ExAC Europe Sub 73354 C=0.99989 G=0.00011
ExAC Asian Sub 25160 C=0.98303 G=0.01697
ExAC American Sub 11578 C=0.99983 G=0.00017
ExAC African Sub 10404 C=1.00000 G=0.00000
ExAC Other Sub 908 C=0.997 G=0.003
gnomAD - Genomes Global Study-wide 31402 C=0.99669 G=0.00331
gnomAD - Genomes European Sub 18904 C=0.99984 G=0.00016
gnomAD - Genomes African Sub 8712 C=0.9999 G=0.0001
gnomAD - Genomes East Asian Sub 1560 C=0.9372 G=0.0628
gnomAD - Genomes Other Sub 1088 C=0.9982 G=0.0018
gnomAD - Genomes American Sub 848 C=1.000 G=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99985 G=0.00015
GO Exome Sequencing Project European American Sub 8600 C=0.9998 G=0.0002
GO Exome Sequencing Project African American Sub 4406 C=1.0000 G=0.0000
ALFA Total Global 11176 C=0.99973 G=0.00027
ALFA European Sub 8134 C=1.0000 G=0.0000
ALFA Other Sub 2302 C=0.9991 G=0.0009
ALFA African Sub 676 C=1.000 G=0.000
ALFA Asian Sub 60 C=0.98 G=0.02
ALFA South Asian Sub 4 C=1.0 G=0.0
ALFA Latin American 1 Sub 0 C=0 G=0
ALFA Latin American 2 Sub 0 C=0 G=0
1000Genomes Global Study-wide 5008 C=0.9890 G=0.0110
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=0.9494 G=0.0506
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=0.996 G=0.004
1000Genomes American Sub 694 C=1.000 G=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 G=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 G=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9593 G=0.0407
Korean Genome Project KOREAN Study-wide 1832 C=0.9749 G=0.0251
A Vietnamese Genetic Variation Database Global Study-wide 613 C=0.927 G=0.073
SGDP_PRJ Global Study-wide 14 C=0.50 G=0.50
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= G
GRCh38.p12 chr 10 NC_000010.11:g.87864461= NC_000010.11:g.87864461C>G
GRCh37.p13 chr 10 NC_000010.10:g.89624218= NC_000010.10:g.89624218C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.6023= NG_007466.2:g.6023C>G
PTEN transcript variant 1 NM_000314.8:c.-9= NM_000314.8:c.-9C>G
PTEN transcript variant 1 NM_000314.7:c.-9= NM_000314.7:c.-9C>G
PTEN transcript variant 1 NM_000314.6:c.-9= NM_000314.6:c.-9C>G
PTEN transcript NM_000314.4:c.-9= NM_000314.4:c.-9C>G
PTEN transcript variant 1 NM_001304717.5:c.511= NM_001304717.5:c.511C>G
PTEN transcript variant 1 NM_001304717.4:c.511= NM_001304717.4:c.511C>G
PTEN transcript variant 1 NM_001304717.3:c.511= NM_001304717.3:c.511C>G
PTEN transcript variant 1 NM_001304717.2:c.511= NM_001304717.2:c.511C>G
PTEN transcript variant 2 NM_001304718.2:c.-714= NM_001304718.2:c.-714C>G
PTEN transcript variant 2 NM_001304718.1:c.-714= NM_001304718.1:c.-714C>G
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.3977= NG_033079.1:g.3977G>C
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.80284= NW_013171807.1:g.80284C>G
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Leu171= NP_001291646.4:p.Leu171Val
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.2:p.Leu171= NP_001291646.2:p.Leu171Val
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#.

33 SubSNP, 14 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16023862 Feb 27, 2004 (120)
2 SC_SNP ss18430194 Feb 27, 2004 (120)
3 IMCJ-GDT ss28503391 Sep 24, 2004 (126)
4 EGP_SNPS ss38349671 Mar 10, 2006 (126)
5 SNP500CANCER ss48296534 Mar 10, 2006 (126)
6 1000GENOMES ss336288984 May 09, 2011 (134)
7 GMI ss475759981 May 04, 2012 (137)
8 ILLUMINA ss534648741 Sep 08, 2015 (146)
9 NHLBI-ESP ss712961380 Apr 25, 2013 (138)
10 JMKIDD_LAB ss1067514454 Aug 21, 2014 (142)
11 1000GENOMES ss1338437068 Aug 21, 2014 (142)
12 EVA_UK10K_ALSPAC ss1625093241 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1668087274 Apr 01, 2015 (144)
14 EVA_EXAC ss1689987190 Apr 01, 2015 (144)
15 HUMAN_LONGEVITY ss2176762875 Dec 20, 2016 (150)
16 TOPMED ss2339866215 Dec 20, 2016 (150)
17 GRF ss2698815670 Nov 08, 2017 (151)
18 GNOMAD ss2738382452 Nov 08, 2017 (151)
19 GNOMAD ss2748430598 Nov 08, 2017 (151)
20 GNOMAD ss2891600731 Nov 08, 2017 (151)
21 ILLUMINA ss3021260730 Nov 08, 2017 (151)
22 TOPMED ss3126304369 Nov 08, 2017 (151)
23 ILLUMINA ss3626499341 Oct 12, 2018 (152)
24 OMUKHERJEE_ADBS ss3646412915 Oct 12, 2018 (152)
25 ILLUMINA ss3651618436 Oct 12, 2018 (152)
26 EGCUT_WGS ss3674298544 Jul 13, 2019 (153)
27 ILLUMINA ss3725175696 Jul 13, 2019 (153)
28 EVA ss3748411500 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3813778969 Jul 13, 2019 (153)
30 EVA ss3824535866 Apr 26, 2020 (154)
31 SGDP_PRJ ss3874732512 Apr 26, 2020 (154)
32 KRGDB ss3922848181 Apr 26, 2020 (154)
33 KOGIC ss3968369668 Apr 26, 2020 (154)
34 1000Genomes NC_000010.10 - 89624218 Oct 12, 2018 (152)
35 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89624218 Oct 12, 2018 (152)
36 Genetic variation in the Estonian population NC_000010.10 - 89624218 Oct 12, 2018 (152)
37 ExAC NC_000010.10 - 89624218 Oct 12, 2018 (152)
38 gnomAD - Genomes NC_000010.10 - 89624218 Jul 13, 2019 (153)
39 gnomAD - Exomes NC_000010.10 - 89624218 Jul 13, 2019 (153)
40 GO Exome Sequencing Project NC_000010.10 - 89624218 Oct 12, 2018 (152)
41 KOREAN population from KRGDB NC_000010.10 - 89624218 Apr 26, 2020 (154)
42 Korean Genome Project NC_000010.11 - 87864461 Apr 26, 2020 (154)
43 SGDP_PRJ NC_000010.10 - 89624218 Apr 26, 2020 (154)
44 TopMed NC_000010.11 - 87864461 Oct 12, 2018 (152)
45 UK 10K study - Twins NC_000010.10 - 89624218 Oct 12, 2018 (152)
46 A Vietnamese Genetic Variation Database NC_000010.10 - 89624218 Jul 13, 2019 (153)
47 dbGaP Population Frequency Project NC_000010.11 - 87864461 Apr 26, 2020 (154)
48 ClinVar RCV000078600.6 Apr 26, 2020 (154)
49 ClinVar RCV000131696.2 Oct 12, 2018 (152)
50 ClinVar RCV000203697.3 Oct 12, 2018 (152)
51 ClinVar RCV000409463.1 Oct 12, 2018 (152)
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)
rs17849089 Mar 10, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss475759981 NC_000010.9:89614197:C:G NC_000010.11:87864460:C:G (self)
50861369, 28232193, 20036792, 214591, 138955111, 7581372, 993552, 30025575, 26749492, 28232193, 6269821, ss336288984, ss534648741, ss712961380, ss1067514454, ss1338437068, ss1625093241, ss1668087274, ss1689987190, ss2339866215, ss2698815670, ss2738382452, ss2748430598, ss2891600731, ss3021260730, ss3626499341, ss3646412915, ss3651618436, ss3674298544, ss3748411500, ss3824535866, ss3874732512, ss3922848181 NC_000010.10:89624217:C:G NC_000010.11:87864460:C:G (self)
RCV000078600.6, RCV000131696.2, RCV000203697.3, RCV000409463.1, 24747669, 48115574, 640169534, ss2176762875, ss3126304369, ss3725175696, ss3813778969, ss3968369668 NC_000010.11:87864460:C:G NC_000010.11:87864460:C:G (self)
ss16023862, ss18430194 NT_030059.11:8372733:C:G NC_000010.11:87864460:C:G (self)
ss28503391, ss38349671, ss48296534 NT_030059.13:40428681:C:G NC_000010.11:87864460:C:G (self)
Help

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

6 citations for rs11202592
PMID Title Author Year Journal
14623110 Association of the polymorphisms in the 5'-untranslated region of PTEN gene with type 2 diabetes in a Japanese population. Ishihara H et al. 2003 FEBS letters
23315997 RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Sabarinathan R et al. 2013 Human mutation
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
24632578 Combined effects of genetic variants of the PTEN, AKT1, MDM2 and p53 genes on the risk of nasopharyngeal carcinoma. Zhang X et al. 2014 PloS one
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
26695147 PTEN polymorphisms contribute to clinical outcomes of advanced lung adenocarcinoma patients treated with platinum-based chemotherapy. Yang Y et al. 2016 Tumour biology
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.post565+e32b82c