Name: rs2736627
Published: September 21, 2022
License: Open Access

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.

rs2736627

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:87961337 (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: C=0.077672 (20559/264690, TOPMED)
C=0.079917 (11202/140170, GnomAD)
C=0.00000 (0/28258, 14KJPN) (+ 17 more)
C=0.09894 (1869/18890, ALFA)
C=0.00006 (1/16760, 8.3KJPN)
C=0.0451 (289/6404, 1000G_30x)
C=0.0457 (229/5008, 1000G)
C=0.1261 (565/4480, Estonian)
C=0.1098 (423/3854, ALSPAC)
C=0.1230 (456/3708, TWINSUK)
C=0.0000 (0/2930, KOREAN)
C=0.0000 (0/1832, Korea1K)
C=0.119 (119/998, GoNL)
C=0.087 (52/600, NorthernSweden)
C=0.040 (22/556, SGDP_PRJ)
C=0.025 (8/326, HapMap)
C=0.106 (23/216, Qatari)
C=0.000 (0/212, Vietnamese)
C=0.05 (3/56, Siberian)
C=0.07 (3/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: PTEN : Intron Variant
Publications: 3 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	C=0.09894	T=0.90106	0.011964	0.814082	0.173954	4
European	Sub	14286	C=0.11823	T=0.88177	0.01498	0.778524	0.206496	0
African	Sub	2946	C=0.0173	T=0.9827	0.000679	0.966056	0.033265	0
African Others	Sub	114	C=0.000	T=1.000	0.0	1.0	0.0	N/A
African American	Sub	2832	C=0.0180	T=0.9820	0.000706	0.964689	0.034605	0
Asian	Sub	112	C=0.000	T=1.000	0.0	1.0	0.0	N/A
East Asian	Sub	86	C=0.00	T=1.00	0.0	1.0	0.0	N/A
Other Asian	Sub	26	C=0.00	T=1.00	0.0	1.0	0.0	N/A
Latin American 1	Sub	146	C=0.096	T=0.904	0.0	0.808219	0.191781	1
Latin American 2	Sub	610	C=0.087	T=0.913	0.006557	0.832787	0.160656	0
South Asian	Sub	98	C=0.04	T=0.96	0.0	0.918367	0.081633	0
Other	Sub	692	C=0.084	T=0.916	0.008671	0.84104	0.150289	0

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.077672	T=0.922328
gnomAD - Genomes	Global	Study-wide	140170	C=0.079917	T=0.920083
gnomAD - Genomes	European	Sub	75904	C=0.11085	T=0.88915
gnomAD - Genomes	African	Sub	42016	C=0.01868	T=0.98132
gnomAD - Genomes	American	Sub	13644	C=0.09425	T=0.90575
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.1631	T=0.8369
gnomAD - Genomes	East Asian	Sub	3132	C=0.0000	T=1.0000
gnomAD - Genomes	Other	Sub	2150	C=0.0814	T=0.9186
14KJPN	JAPANESE	Study-wide	28258	C=0.00000	T=1.00000
Allele Frequency Aggregator	Total	Global	18890	C=0.09894	T=0.90106
Allele Frequency Aggregator	European	Sub	14286	C=0.11823	T=0.88177
Allele Frequency Aggregator	African	Sub	2946	C=0.0173	T=0.9827
Allele Frequency Aggregator	Other	Sub	692	C=0.084	T=0.916
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.087	T=0.913
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.096	T=0.904
Allele Frequency Aggregator	Asian	Sub	112	C=0.000	T=1.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.04	T=0.96
8.3KJPN	JAPANESE	Study-wide	16760	C=0.00006	T=0.99994
1000Genomes_30x	Global	Study-wide	6404	C=0.0451	T=0.9549
1000Genomes_30x	African	Sub	1786	C=0.0050	T=0.9950
1000Genomes_30x	Europe	Sub	1266	C=0.1185	T=0.8815
1000Genomes_30x	South Asian	Sub	1202	C=0.0283	T=0.9717
1000Genomes_30x	East Asian	Sub	1170	C=0.0000	T=1.0000
1000Genomes_30x	American	Sub	980	C=0.098	T=0.902
1000Genomes	Global	Study-wide	5008	C=0.0457	T=0.9543
1000Genomes	African	Sub	1322	C=0.0053	T=0.9947
1000Genomes	East Asian	Sub	1008	C=0.0000	T=1.0000
1000Genomes	Europe	Sub	1006	C=0.1193	T=0.8807
1000Genomes	South Asian	Sub	978	C=0.032	T=0.968
1000Genomes	American	Sub	694	C=0.102	T=0.898
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.1261	T=0.8739
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.1098	T=0.8902
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.1230	T=0.8770
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0000	T=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0000	T=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.119	T=0.881
Northern Sweden	ACPOP	Study-wide	600	C=0.087	T=0.913
SGDP_PRJ	Global	Study-wide	556	C=0.040	T=0.960
HapMap	Global	Study-wide	326	C=0.025	T=0.975
HapMap	African	Sub	118	C=0.000	T=1.000
HapMap	American	Sub	118	C=0.068	T=0.932
HapMap	Asian	Sub	90	C=0.00	T=1.00
Qatari	Global	Study-wide	216	C=0.106	T=0.894
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.000	T=1.000
Siberian	Global	Study-wide	56	C=0.05	T=0.95
The Danish reference pan genome	Danish	Study-wide	40	C=0.07	T=0.93

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 10	NC_000010.11:g.87961337C>T
GRCh37.p13 chr 10	NC_000010.10:g.89721094C>T
PTEN RefSeqGene (LRG_311)	NG_007466.2:g.102899C>T
GRCh38.p14 chr 10 fix patch HG2334_PATCH	NW_013171807.1:g.177126C>T

Gene: PTEN, phosphatase and tensin homolog (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTEN transcript variant 1	NM_000314.8:c.1026+219C>T	N/A	Intron Variant
PTEN transcript variant 2	NM_001304717.5:c.1546+219… NM_001304717.5:c.1546+219C>T	N/A	Intron Variant
PTEN transcript variant 3	NM_001304718.2:c.435+219C… NM_001304718.2:c.435+219C>T	N/A	Intron Variant

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: 1235275 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001648691.2	not provided	Benign

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 10	NC_000010.11:g.87961337=	NC_000010.11:g.87961337C>T
GRCh37.p13 chr 10	NC_000010.10:g.89721094=	NC_000010.10:g.89721094C>T
PTEN RefSeqGene (LRG_311)	NG_007466.2:g.102899=	NG_007466.2:g.102899C>T
GRCh38.p14 chr 10 fix patch HG2334_PATCH	NW_013171807.1:g.177126=	NW_013171807.1:g.177126C>T
PTEN transcript	NM_000314.4:c.1026+219=	NM_000314.4:c.1026+219C>T
PTEN transcript variant 1	NM_000314.8:c.1026+219=	NM_000314.8:c.1026+219C>T
PTEN transcript variant 2	NM_001304717.5:c.1546+219=	NM_001304717.5:c.1546+219C>T
PTEN transcript variant 3	NM_001304718.2:c.435+219=	NM_001304718.2:c.435+219C>T

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#.

82 SubSNP, 20 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3863237	Sep 28, 2001 (100)
2	WI_SSAHASNP	ss6822103	Feb 20, 2003 (111)
3	SC_SNP	ss12977536	Dec 05, 2003 (119)
4	WI_SSAHASNP	ss14421832	Dec 05, 2003 (119)
5	SC_SNP	ss15999427	Feb 27, 2004 (120)
6	SSAHASNP	ss20686725	Apr 05, 2004 (121)
7	PERLEGEN	ss24541404	Sep 20, 2004 (123)
8	EGP_SNPS	ss38349836	Mar 14, 2006 (126)
9	HGSV	ss85845170	Dec 14, 2007 (130)
10	BCMHGSC_JDW	ss88301791	Mar 23, 2008 (129)
11	HUMANGENOME_JCVI	ss97573559	Feb 03, 2009 (130)
12	BGI	ss106692308	Feb 03, 2009 (130)
13	1000GENOMES	ss109634377	Jan 24, 2009 (130)
14	1000GENOMES	ss113609680	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss119257677	Feb 15, 2009 (130)
16	ENSEMBL	ss131996505	Dec 01, 2009 (131)
17	ENSEMBL	ss137902035	Dec 01, 2009 (131)
18	GMI	ss155345529	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss168658772	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss170682327	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss174678703	Jul 04, 2010 (132)
22	BUSHMAN	ss201828344	Jul 04, 2010 (132)
23	BCM-HGSC-SUB	ss207182512	Jul 04, 2010 (132)
24	1000GENOMES	ss224860490	Jul 14, 2010 (132)
25	1000GENOMES	ss235274497	Jul 15, 2010 (132)
26	1000GENOMES	ss241961753	Jul 15, 2010 (132)
27	BL	ss254496991	May 09, 2011 (134)
28	GMI	ss280714854	May 04, 2012 (137)
29	GMI	ss286235663	Apr 25, 2013 (138)
30	PJP	ss290890285	May 09, 2011 (134)
31	ILLUMINA	ss410925458	Sep 17, 2011 (135)
32	TISHKOFF	ss562115211	Apr 25, 2013 (138)
33	SSMP	ss657123243	Apr 25, 2013 (138)
34	EVA-GONL	ss987754565	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1077180461	Aug 21, 2014 (142)
36	1000GENOMES	ss1338439515	Aug 21, 2014 (142)
37	DDI	ss1426397487	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1575269322	Apr 01, 2015 (144)
39	EVA_DECODE	ss1597427329	Apr 01, 2015 (144)
40	EVA_UK10K_ALSPAC	ss1625094749	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1668088782	Apr 01, 2015 (144)
42	HAMMER_LAB	ss1806500743	Sep 08, 2015 (146)
43	WEILL_CORNELL_DGM	ss1931122842	Feb 12, 2016 (147)
44	GENOMED	ss1967189166	Jul 19, 2016 (147)
45	JJLAB	ss2026289176	Sep 14, 2016 (149)
46	USC_VALOUEV	ss2154564560	Dec 20, 2016 (150)
47	HUMAN_LONGEVITY	ss2176768538	Dec 20, 2016 (150)
48	SYSTEMSBIOZJU	ss2627613666	Nov 08, 2017 (151)
49	GRF	ss2698815875	Nov 08, 2017 (151)
50	GNOMAD	ss2891608132	Nov 08, 2017 (151)
51	SWEGEN	ss3006889926	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3026934155	Nov 08, 2017 (151)
53	CSHL	ss3349240475	Nov 08, 2017 (151)
54	URBANLAB	ss3649431388	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3674299697	Jul 13, 2019 (153)
56	EVA_DECODE	ss3690369991	Jul 13, 2019 (153)
57	ACPOP	ss3737543940	Jul 13, 2019 (153)
58	EVA	ss3748412256	Jul 13, 2019 (153)
59	PACBIO	ss3786744150	Jul 13, 2019 (153)
60	PACBIO	ss3791913894	Jul 13, 2019 (153)
61	PACBIO	ss3796796001	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3813779672	Jul 13, 2019 (153)
63	EVA	ss3832252769	Apr 26, 2020 (154)
64	EVA	ss3839667022	Apr 26, 2020 (154)
65	EVA	ss3845140440	Apr 26, 2020 (154)
66	SGDP_PRJ	ss3874733701	Apr 26, 2020 (154)
67	KRGDB	ss3922849606	Apr 26, 2020 (154)
68	KOGIC	ss3968370636	Apr 26, 2020 (154)
69	TOPMED	ss4861021076	Apr 26, 2021 (155)
70	TOMMO_GENOMICS	ss5198762860	Apr 26, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5284928944	Oct 16, 2022 (156)
72	EVA	ss5395036032	Oct 16, 2022 (156)
73	HUGCELL_USP	ss5480404994	Oct 16, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5579324697	Oct 16, 2022 (156)
75	SANFORD_IMAGENETICS	ss5649795863	Oct 16, 2022 (156)
76	TOMMO_GENOMICS	ss5744919214	Oct 16, 2022 (156)
77	YY_MCH	ss5811752953	Oct 16, 2022 (156)
78	EVA	ss5824744273	Oct 16, 2022 (156)
79	EVA	ss5849676245	Oct 16, 2022 (156)
80	EVA	ss5879900060	Oct 16, 2022 (156)
81	EVA	ss5941076837	Oct 16, 2022 (156)
82	EVA	ss5980628635	Oct 16, 2022 (156)
83	1000Genomes	NC_000010.10 - 89721094	Oct 12, 2018 (152)
84	1000Genomes_30x	NC_000010.11 - 87961337	Oct 16, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 89721094	Oct 12, 2018 (152)
86	Genetic variation in the Estonian population	NC_000010.10 - 89721094	Oct 12, 2018 (152)
87	The Danish reference pan genome	NC_000010.10 - 89721094	Apr 26, 2020 (154)
88	gnomAD - Genomes	NC_000010.11 - 87961337	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000010.10 - 89721094	Apr 26, 2020 (154)
90	HapMap	NC_000010.11 - 87961337	Apr 26, 2020 (154)
91	KOREAN population from KRGDB	NC_000010.10 - 89721094	Apr 26, 2020 (154)
92	Korean Genome Project	NC_000010.11 - 87961337	Apr 26, 2020 (154)
93	Northern Sweden	NC_000010.10 - 89721094	Jul 13, 2019 (153)
94	Qatari	NC_000010.10 - 89721094	Apr 26, 2020 (154)
95	SGDP_PRJ	NC_000010.10 - 89721094	Apr 26, 2020 (154)
96	Siberian	NC_000010.10 - 89721094	Apr 26, 2020 (154)
97	8.3KJPN	NC_000010.10 - 89721094	Apr 26, 2021 (155)
98	14KJPN	NC_000010.11 - 87961337	Oct 16, 2022 (156)
99	TopMed	NC_000010.11 - 87961337	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000010.10 - 89721094	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000010.10 - 89721094	Jul 13, 2019 (153)
102	ALFA	NC_000010.11 - 87961337	Apr 26, 2021 (155)
103	ClinVar	RCV001648691.2	Oct 16, 2022 (156)

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)
rs17431225	Oct 08, 2004 (123)
rs56736502	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85845170	NC_000010.8:89711073:C:T	NC_000010.11:87961336:C:T	(self)
ss88301791, ss109634377, ss113609680, ss119257677, ss168658772, ss170682327, ss174678703, ss201828344, ss207182512, ss254496991, ss280714854, ss286235663, ss290890285, ss1597427329	NC_000010.9:89711073:C:T	NC_000010.11:87961336:C:T	(self)
50863936, 28233850, 20037945, 2263940, 12590561, 30027000, 10828805, 13164772, 26750681, 7080914, 56732167, 28233850, 6270191, ss224860490, ss235274497, ss241961753, ss562115211, ss657123243, ss987754565, ss1077180461, ss1338439515, ss1426397487, ss1575269322, ss1625094749, ss1668088782, ss1806500743, ss1931122842, ss1967189166, ss2026289176, ss2154564560, ss2627613666, ss2698815875, ss2891608132, ss3006889926, ss3349240475, ss3674299697, ss3737543940, ss3748412256, ss3786744150, ss3791913894, ss3796796001, ss3832252769, ss3839667022, ss3874733701, ss3922849606, ss5198762860, ss5395036032, ss5649795863, ss5824744273, ss5941076837, ss5980628635	NC_000010.10:89721093:C:T	NC_000010.11:87961336:C:T	(self)
RCV001648691.2, 66850632, 359401291, 457894, 24748637, 78756318, 76566731, 7729588124, ss2176768538, ss3026934155, ss3649431388, ss3690369991, ss3813779672, ss3845140440, ss3968370636, ss4861021076, ss5284928944, ss5480404994, ss5579324697, ss5744919214, ss5811752953, ss5849676245, ss5879900060	NC_000010.11:87961336:C:T	NC_000010.11:87961336:C:T	(self)
ss12977536	NT_030059.10:8159641:C:T	NC_000010.11:87961336:C:T	(self)
ss15999427, ss20686725	NT_030059.11:8469609:C:T	NC_000010.11:87961336:C:T	(self)
ss3863237, ss6822103, ss14421832, ss24541404, ss38349836, ss97573559, ss106692308, ss131996505, ss137902035, ss155345529, ss410925458	NT_030059.13:40525557:C:T	NC_000010.11:87961336:C:T	(self)

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

3 citations for rs2736627

PMID	Title	Author	Year	Journal
18805939	Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis.	Tempfer CB et al.	2009	Human reproduction update
21093899	Endometrial cancer and genetic variation in PTEN, PIK3CA, AKT1, MLH1, and MSH2 within a population-based case-control study.	Lacey JV Jr et al.	2011	Gynecologic oncology
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

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2736627