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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.

rs12573787

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87863959 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.134915 (16941/125568, TOPMED)
A=0.1603 (803/5008, 1000G)
A=0.1070 (479/4478, Estonian) (+ 10 more)
A=0.1463 (564/3854, ALSPAC)
A=0.1529 (567/3708, TWINSUK)
A=0.3375 (976/2892, KOREAN)
A=0.1572 (344/2188, ALFA Project)
A=0.3414 (603/1766, Korea1K)
A=0.142 (85/600, NorthernSweden)
A=0.079 (17/216, Qatari)
G=0.371 (66/178, SGDP_PRJ)
A=0.28 (11/40, GENOME_DK)
G=0.44 (7/16, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Missense Variant
KLLN : 2KB Upstream Variant
Publications
4 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.87863959G>A
GRCh38.p12 chr 10 NC_000010.11:g.87863959G>C
GRCh37.p13 chr 10 NC_000010.10:g.89623716G>A
GRCh37.p13 chr 10 NC_000010.10:g.89623716G>C
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5522G>A
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5522G>C
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4479C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4479C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79783G>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79783G>C
Gene: PTEN, phosphatase and tensin homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 2 NM_001304718.2:c.-1215= N/A 5 Prime UTR Variant
PTEN transcript variant 1 NM_000314.8:c.-511= N/A 5 Prime UTR Variant
PTEN transcript variant 1 NM_001304717.5:c.10G>A G [GGG] > R [AGG] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Gly4Arg G (Gly) > R (Arg) Missense Variant
PTEN transcript variant 1 NM_001304717.5:c.10G>C G [GGG] > R [CGG] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Gly4Arg G (Gly) > R (Arg) 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: A (allele ID: 799618 )
ClinVar Accession Disease Names Clinical Significance
RCV001000222.1 not specified 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 15966 G=0.94012 A=0.05988, C=0.00000
European Sub 12340 G=0.92658 A=0.07342, C=0.00000
African Sub 2642 G=0.9830 A=0.0170, C=0.0000
African Others Sub 104 G=1.000 A=0.000, C=0.000
African American Sub 2538 G=0.9823 A=0.0177, C=0.0000
Asian Sub 50 G=0.96 A=0.04, C=0.00
East Asian Sub 36 G=0.97 A=0.03, C=0.00
Other Asian Sub 14 G=0.93 A=0.07, C=0.00
Latin American 1 Sub 114 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 366 G=1.000 A=0.000, C=0.000
South Asian Sub 74 G=1.00 A=0.00, C=0.00
Other Sub 380 G=0.992 A=0.008, C=0.000


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 125568 G=0.865085 A=0.134915
1000Genomes Global Study-wide 5008 G=0.8397 A=0.1603
1000Genomes African Sub 1322 G=0.9425 A=0.0575
1000Genomes East Asian Sub 1008 G=0.6687 A=0.3313
1000Genomes Europe Sub 1006 G=0.8698 A=0.1302
1000Genomes South Asian Sub 978 G=0.872 A=0.128
1000Genomes American Sub 694 G=0.803 A=0.197
Genetic variation in the Estonian population Estonian Study-wide 4478 G=0.8930 A=0.1070
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8537 A=0.1463
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8471 A=0.1529
KOREAN population from KRGDB KOREAN Study-wide 2892 G=0.6625 A=0.3375
ALFA Total Global 2188 G=0.8428 A=0.1572
ALFA European Sub 2072 G=0.8383 A=0.1617
ALFA African Sub 82 G=0.94 A=0.06
ALFA Other Sub 26 G=0.92 A=0.08
ALFA South Asian Sub 4 G=1.0 A=0.0
ALFA Asian Sub 4 G=0.5 A=0.5
ALFA Latin American 1 Sub 0 G=0 A=0
ALFA Latin American 2 Sub 0 G=0 A=0
Korean Genome Project KOREAN Study-wide 1766 G=0.6586 A=0.3414
Northern Sweden ACPOP Study-wide 600 G=0.858 A=0.142
Qatari Global Study-wide 216 G=0.921 A=0.079
SGDP_PRJ Global Study-wide 178 G=0.371 A=0.629
The Danish reference pan genome Danish Study-wide 40 G=0.72 A=0.28
Siberian Global Study-wide 16 G=0.44 A=0.56
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
GRCh38.p12 chr 10 NC_000010.11:g.87863959= NC_000010.11:g.87863959G>A NC_000010.11:g.87863959G>C
GRCh37.p13 chr 10 NC_000010.10:g.89623716= NC_000010.10:g.89623716G>A NC_000010.10:g.89623716G>C
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5522= NG_007466.2:g.5522G>A NG_007466.2:g.5522G>C
PTEN transcript variant 1 NM_000314.8:c.-511= NM_000314.8:c.-511G>A NM_000314.8:c.-511G>C
PTEN transcript variant 1 NM_000314.7:c.-510= NM_000314.7:c.-510G>A NM_000314.7:c.-510G>C
PTEN transcript variant 1 NM_000314.6:c.-510= NM_000314.6:c.-510G>A NM_000314.6:c.-510G>C
PTEN transcript NM_000314.4:c.-510= NM_000314.4:c.-510G>A NM_000314.4:c.-510G>C
PTEN transcript variant 1 NM_001304717.5:c.10= NM_001304717.5:c.10G>A NM_001304717.5:c.10G>C
PTEN transcript variant 1 NM_001304717.4:c.10= NM_001304717.4:c.10G>A NM_001304717.4:c.10G>C
PTEN transcript variant 1 NM_001304717.3:c.10= NM_001304717.3:c.10G>A NM_001304717.3:c.10G>C
PTEN transcript variant 1 NM_001304717.2:c.10= NM_001304717.2:c.10G>A NM_001304717.2:c.10G>C
PTEN transcript variant 2 NM_001304718.2:c.-1215= NM_001304718.2:c.-1215G>A NM_001304718.2:c.-1215G>C
PTEN transcript variant 2 NM_001304718.1:c.-1215= NM_001304718.1:c.-1215G>A NM_001304718.1:c.-1215G>C
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4479= NG_033079.1:g.4479C>T NG_033079.1:g.4479C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79783= NW_013171807.1:g.79783G>A NW_013171807.1:g.79783G>C
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Gly4= NP_001291646.4:p.Gly4Arg NP_001291646.4:p.Gly4Arg
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.2:p.Gly4= NP_001291646.2:p.Gly4Arg NP_001291646.2:p.Gly4Arg
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#.

29 SubSNP, 15 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19901111 Feb 28, 2004 (120)
2 EGP_SNPS ss38349670 Mar 13, 2006 (126)
3 1000GENOMES ss336288983 May 09, 2011 (134)
4 SSMP ss657122677 Apr 25, 2013 (138)
5 EVA-GONL ss987753820 Aug 21, 2014 (142)
6 1000GENOMES ss1338437054 Aug 21, 2014 (142)
7 EVA_GENOME_DK ss1575269147 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1625093239 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1668087272 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1931122227 Feb 12, 2016 (147)
11 JJLAB ss2026288825 Sep 14, 2016 (149)
12 USC_VALOUEV ss2154564354 Dec 20, 2016 (150)
13 TOPMED ss2339866183 Dec 20, 2016 (150)
14 GRF ss2698815668 Nov 08, 2017 (151)
15 GNOMAD ss2891600674 Nov 08, 2017 (151)
16 TOPMED ss3126304209 Nov 08, 2017 (151)
17 CSHL ss3349240367 Nov 08, 2017 (151)
18 OMUKHERJEE_ADBS ss3646412913 Oct 12, 2018 (152)
19 EGCUT_WGS ss3674298537 Jul 13, 2019 (153)
20 EVA_DECODE ss3690368809 Jul 13, 2019 (153)
21 ACPOP ss3737543556 Jul 13, 2019 (153)
22 EVA ss3748411488 Jul 13, 2019 (153)
23 PACBIO ss3786744068 Jul 13, 2019 (153)
24 PACBIO ss3791913849 Jul 13, 2019 (153)
25 PACBIO ss3796795957 Jul 13, 2019 (153)
26 KHV_HUMAN_GENOMES ss3813778964 Jul 13, 2019 (153)
27 SGDP_PRJ ss3874732500 Apr 26, 2020 (154)
28 KRGDB ss3922848172 Apr 26, 2020 (154)
29 KOGIC ss3968369654 Apr 26, 2020 (154)
30 1000Genomes NC_000010.10 - 89623716 Oct 12, 2018 (152)
31 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89623716 Oct 12, 2018 (152)
32 Genetic variation in the Estonian population NC_000010.10 - 89623716 Oct 12, 2018 (152)
33 The Danish reference pan genome NC_000010.10 - 89623716 Apr 26, 2020 (154)
34 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138955047 (NC_000010.10:89623715:G:G 26921/30540, NC_000010.10:89623715:G:A 3619/30540)
Row 138955048 (NC_000010.10:89623715:G:G 30539/30540, NC_000010.10:89623715:G:C 1/30540)

- Jul 13, 2019 (153)
35 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138955047 (NC_000010.10:89623715:G:G 26921/30540, NC_000010.10:89623715:G:A 3619/30540)
Row 138955048 (NC_000010.10:89623715:G:G 30539/30540, NC_000010.10:89623715:G:C 1/30540)

- Jul 13, 2019 (153)
36 KOREAN population from KRGDB NC_000010.10 - 89623716 Apr 26, 2020 (154)
37 Korean Genome Project NC_000010.11 - 87863959 Apr 26, 2020 (154)
38 Northern Sweden NC_000010.10 - 89623716 Jul 13, 2019 (153)
39 Qatari NC_000010.10 - 89623716 Apr 26, 2020 (154)
40 SGDP_PRJ NC_000010.10 - 89623716 Apr 26, 2020 (154)
41 Siberian NC_000010.10 - 89623716 Apr 26, 2020 (154)
42 TopMed NC_000010.11 - 87863959 Oct 12, 2018 (152)
43 UK 10K study - Twins NC_000010.10 - 89623716 Oct 12, 2018 (152)
44 dbGaP Population Frequency Project NC_000010.11 - 87863959 Apr 26, 2020 (154)
45 ClinVar RCV001000222.1 Apr 26, 2020 (154)
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
50861354, 28232191, 20036785, 2263809, 30025566, 10828421, 13164157, 26749480, 7080708, 28232191, ss336288983, ss657122677, ss987753820, ss1338437054, ss1575269147, ss1625093239, ss1668087272, ss1931122227, ss2026288825, ss2154564354, ss2339866183, ss2698815668, ss2891600674, ss3349240367, ss3646412913, ss3674298537, ss3737543556, ss3748411488, ss3786744068, ss3791913849, ss3796795957, ss3874732500, ss3922848172 NC_000010.10:89623715:G:A NC_000010.11:87863958:G:A (self)
RCV001000222.1, 24747655, 48115450, 408471188, ss3126304209, ss3690368809, ss3813778964, ss3968369654 NC_000010.11:87863958:G:A NC_000010.11:87863958:G:A (self)
ss19901111 NT_030059.11:8372231:G:A NC_000010.11:87863958:G:A (self)
ss38349670 NT_030059.13:40428179:G:A NC_000010.11:87863958:G:A (self)
ss2891600674 NC_000010.10:89623715:G:C NC_000010.11:87863958:G:C (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 rs12573787
PMID Title Author Year Journal
17033968 Mutation-positive and mutation-negative patients with Cowden and Bannayan-Riley-Ruvalcaba syndromes associated with distinct 10q haplotypes. Pezzolesi MG et al. 2006 American journal of human genetics
21633361 Germ-line sequence variants of PTEN do not have an important role in hereditary and non-hereditary prostate cancer susceptibility. Xie CC et al. 2011 Journal of human genetics
22146979 Roles of genetic variants in the PI3K and RAS/RAF pathways in susceptibility to endometrial cancer and clinical outcomes. Wang LE et al. 2012 Journal of cancer research and clinical oncology
30738963 Single nucleotide polymorphism in PTEN-Long gene: A risk factor in chronic myeloid leukemia. Ferri C et al. 2019 Gene
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