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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.

rs2943772

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:87864144 (GRCh38.p13) 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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000008 (2/264690, TOPMED)
G=0.000164 (23/139982, GnomAD)
G=0.00072 (12/16718, 8.3KJPN) (+ 9 more)
G=0.00006 (1/16330, ALFA)
G=0.0000 (0/5008, 1000G)
G=0.0000 (0/2922, KOREAN)
A=0.0000 (0/2922, KOREAN)
T=0.0000 (0/2922, KOREAN)
G=0.000 (0/600, NorthernSweden)
G=0.000 (0/556, SGDP_PRJ)
G=0.00 (0/40, GENOME_DK)
G=0.00 (0/32, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Missense Variant
KLLN : 2KB Upstream Variant
Publications
0 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.p13 chr 10 NC_000010.11:g.87864144G>A
GRCh38.p13 chr 10 NC_000010.11:g.87864144G>C
GRCh38.p13 chr 10 NC_000010.11:g.87864144G>T
GRCh37.p13 chr 10 NC_000010.10:g.89623901G>A
GRCh37.p13 chr 10 NC_000010.10:g.89623901G>C
GRCh37.p13 chr 10 NC_000010.10:g.89623901G>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5706C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5706C>A
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5706C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4294C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4294C>G
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4294C>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79967C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79967C>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79967C>T
Gene: PTEN, phosphatase and tensin homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 1 NM_001304717.5:c.194C>G S [TCC] > C [TGC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Ser65Cys S (Ser) > C (Cys) Missense Variant
PTEN transcript variant 1 NM_001304717.5:c.194C>A S [TCC] > Y [TAC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Ser65Tyr S (Ser) > Y (Tyr) Missense Variant
PTEN transcript variant 1 NM_001304717.5:c.194C>T S [TCC] > F [TTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Ser65Phe S (Ser) > F (Phe) Missense Variant
PTEN transcript variant 2 NM_001304718.2:c.-1031C>G N/A 5 Prime UTR Variant
PTEN transcript variant 1 NM_000314.8:c.-326= N/A 5 Prime UTR 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_001126049.2: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: C (allele ID: 433880 )
ClinVar Accession Disease Names Clinical Significance
RCV000507752.3 none provided 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 16330 G=0.00006 C=0.99994
European Sub 12078 G=0.00008 C=0.99992
African Sub 2816 G=0.0000 C=1.0000
African Others Sub 108 G=0.000 C=1.000
African American Sub 2708 G=0.0000 C=1.0000
Asian Sub 108 G=0.000 C=1.000
East Asian Sub 84 G=0.00 C=1.00
Other Asian Sub 24 G=0.00 C=1.00
Latin American 1 Sub 146 G=0.000 C=1.000
Latin American 2 Sub 610 G=0.000 C=1.000
South Asian Sub 94 G=0.00 C=1.00
Other Sub 478 G=0.000 C=1.000


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 G=0.000008 C=0.999992
gnomAD - Genomes Global Study-wide 139982 G=0.000164 C=0.999836
gnomAD - Genomes European Sub 75764 G=0.00016 C=0.99984
gnomAD - Genomes African Sub 41970 G=0.00019 C=0.99981
gnomAD - Genomes American Sub 13646 G=0.00022 C=0.99978
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.0000 C=1.0000
gnomAD - Genomes East Asian Sub 3132 G=0.0000 C=1.0000
gnomAD - Genomes Other Sub 2146 G=0.0000 C=1.0000
8.3KJPN JAPANESE Study-wide 16718 G=0.00072 C=0.99928
1000Genomes Global Study-wide 5008 G=0.0000 C=1.0000
1000Genomes African Sub 1322 G=0.0000 C=1.0000
1000Genomes East Asian Sub 1008 G=0.0000 C=1.0000
1000Genomes Europe Sub 1006 G=0.0000 C=1.0000
1000Genomes South Asian Sub 978 G=0.000 C=1.000
1000Genomes American Sub 694 G=0.000 C=1.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.0000 A=0.0000, C=1.0000, T=0.0000
Northern Sweden ACPOP Study-wide 600 G=0.000 C=1.000
SGDP_PRJ Global Study-wide 556 G=0.000 C=1.000
The Danish reference pan genome Danish Study-wide 40 G=0.00 C=1.00
Siberian Global Study-wide 32 G=0.00 C=1.00
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 G= A C T
GRCh38.p13 chr 10 NC_000010.11:g.87864144= NC_000010.11:g.87864144G>A NC_000010.11:g.87864144G>C NC_000010.11:g.87864144G>T
GRCh37.p13 chr 10 NC_000010.10:g.89623901= NC_000010.10:g.89623901G>A NC_000010.10:g.89623901G>C NC_000010.10:g.89623901G>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5706C>G NG_007466.2:g.5706C>A NG_007466.2:g.5706= NG_007466.2:g.5706C>T
PTEN transcript variant 1 NM_000314.8:c.-326= NM_000314.8:c.-326G>A NM_000314.8:c.-326G>C NM_000314.8:c.-326G>T
PTEN transcript variant 1 NM_000314.7:c.-326C>G NM_000314.7:c.-326C>A NM_000314.7:c.-326= NM_000314.7:c.-326C>T
PTEN transcript variant 1 NM_000314.6:c.-326C>G NM_000314.6:c.-326C>A NM_000314.6:c.-326= NM_000314.6:c.-326C>T
PTEN transcript NM_000314.4:c.-326C>G NM_000314.4:c.-326C>A NM_000314.4:c.-326= NM_000314.4:c.-326C>T
PTEN transcript variant 1 NM_001304717.5:c.194C>G NM_001304717.5:c.194C>A NM_001304717.5:c.194= NM_001304717.5:c.194C>T
PTEN transcript variant 1 NM_001304717.4:c.194C>G NM_001304717.4:c.194C>A NM_001304717.4:c.194= NM_001304717.4:c.194C>T
PTEN transcript variant 1 NM_001304717.3:c.194C>G NM_001304717.3:c.194C>A NM_001304717.3:c.194= NM_001304717.3:c.194C>T
PTEN transcript variant 1 NM_001304717.2:c.194C>G NM_001304717.2:c.194C>A NM_001304717.2:c.194= NM_001304717.2:c.194C>T
PTEN transcript variant 2 NM_001304718.2:c.-1031C>G NM_001304718.2:c.-1031C>A NM_001304718.2:c.-1031= NM_001304718.2:c.-1031C>T
PTEN transcript variant 2 NM_001304718.1:c.-1031C>G NM_001304718.1:c.-1031C>A NM_001304718.1:c.-1031= NM_001304718.1:c.-1031C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4294= NG_033079.1:g.4294C>T NG_033079.1:g.4294C>G NG_033079.1:g.4294C>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79967C>G NW_013171807.1:g.79967C>A NW_013171807.1:g.79967= NW_013171807.1:g.79967C>T
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Ser65Cys NP_001291646.4:p.Ser65Tyr NP_001291646.4:p.Ser65= NP_001291646.4:p.Ser65Phe
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#.

39 SubSNP, 10 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4150082 Nov 05, 2001 (101)
2 CSHL-HAPMAP ss16510258 Feb 27, 2004 (120)
3 HUMANGENOME_JCVI ss97573551 Feb 05, 2009 (130)
4 ENSEMBL ss137902086 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss170681872 Jul 04, 2010 (132)
6 BUSHMAN ss201828121 Jul 04, 2010 (132)
7 BCM-HGSC-SUB ss207485916 Jul 04, 2010 (132)
8 BL ss254496872 May 09, 2011 (134)
9 PJP ss290890260 May 09, 2011 (134)
10 SSMP ss657122679 Apr 25, 2013 (138)
11 1000GENOMES ss1338437057 Aug 21, 2014 (142)
12 DDI ss1426397429 Apr 01, 2015 (144)
13 EVA_GENOME_DK ss1575269150 Apr 01, 2015 (144)
14 HAMMER_LAB ss1806500650 Sep 08, 2015 (146)
15 JJLAB ss2026288826 Sep 14, 2016 (149)
16 USC_VALOUEV ss2154564359 Dec 20, 2016 (150)
17 HUMAN_LONGEVITY ss2176762849 Dec 20, 2016 (150)
18 GRF ss2698815669 Nov 08, 2017 (151)
19 SWEGEN ss3006888888 Nov 08, 2017 (151)
20 TOPMED ss3126304269 Nov 08, 2017 (151)
21 CSHL ss3349240369 Nov 08, 2017 (151)
22 OMUKHERJEE_ADBS ss3646412914 Oct 12, 2018 (152)
23 URBANLAB ss3649431373 Oct 12, 2018 (152)
24 EVA_DECODE ss3690368819 Jul 13, 2019 (153)
25 ACPOP ss3737543562 Jul 13, 2019 (153)
26 EVA ss3748411494 Jul 13, 2019 (153)
27 PACBIO ss3786744070 Jul 13, 2019 (153)
28 PACBIO ss3791913851 Jul 13, 2019 (153)
29 PACBIO ss3796795959 Jul 13, 2019 (153)
30 KHV_HUMAN_GENOMES ss3813778966 Jul 13, 2019 (153)
31 EVA ss3832252640 Apr 26, 2020 (154)
32 EVA ss3845140400 Apr 26, 2020 (154)
33 SGDP_PRJ ss3874732507 Apr 26, 2020 (154)
34 KRGDB ss3922848176 Apr 26, 2020 (154)
35 FSA-LAB ss3983982129 Apr 26, 2021 (155)
36 EVA ss3986051088 Apr 26, 2021 (155)
37 GNOMAD ss4222814065 Apr 26, 2021 (155)
38 TOPMED ss4860996854 Apr 26, 2021 (155)
39 TOMMO_GENOMICS ss5198759984 Apr 26, 2021 (155)
40 1000Genomes NC_000010.10 - 89623901 Oct 12, 2018 (152)
41 The Danish reference pan genome NC_000010.10 - 89623901 Apr 26, 2020 (154)
42 gnomAD - Genomes NC_000010.11 - 87864144 Apr 26, 2021 (155)
43 KOREAN population from KRGDB NC_000010.10 - 89623901 Apr 26, 2020 (154)
44 Northern Sweden NC_000010.10 - 89623901 Jul 13, 2019 (153)
45 SGDP_PRJ NC_000010.10 - 89623901 Apr 26, 2020 (154)
46 Siberian NC_000010.10 - 89623901 Apr 26, 2020 (154)
47 8.3KJPN NC_000010.10 - 89623901 Apr 26, 2021 (155)
48 TopMed NC_000010.11 - 87864144 Apr 26, 2021 (155)
49 ALFA NC_000010.11 - 87864144 Apr 26, 2021 (155)
50 ClinVar RCV000507752.3 Apr 26, 2021 (155)
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
30025570, ss3922848176 NC_000010.10:89623900:G:A NC_000010.11:87864143:G:A (self)
ss170681872, ss201828121, ss207485916, ss254496872, ss290890260 NC_000010.9:89613880:G:C NC_000010.11:87864143:G:C (self)
50861358, 2263810, 30025570, 10828427, 26749487, 7080713, 56729291, ss657122679, ss1338437057, ss1426397429, ss1575269150, ss1806500650, ss2026288826, ss2154564359, ss2698815669, ss3006888888, ss3349240369, ss3646412914, ss3737543562, ss3748411494, ss3786744070, ss3791913851, ss3796795959, ss3832252640, ss3874732507, ss3922848176, ss3983982129, ss3986051088, ss5198759984 NC_000010.10:89623900:G:C NC_000010.11:87864143:G:C (self)
RCV000507752.3, 359381766, 76542509, 3439239461, ss2176762849, ss3126304269, ss3649431373, ss3690368819, ss3813778966, ss3845140400, ss4222814065, ss4860996854 NC_000010.11:87864143:G:C NC_000010.11:87864143:G:C (self)
ss16510258 NT_030059.11:8372416:G:C NC_000010.11:87864143:G:C (self)
ss4150082, ss97573551, ss137902086 NT_030059.13:40428364:G:C NC_000010.11:87864143:G:C (self)
30025570, ss3922848176 NC_000010.10:89623900:G:T NC_000010.11:87864143:G: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 rs2943772

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.post596+ae089ad