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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.

rs555895

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87961150 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.373306 (92706/248338, GnomAD_exome)
G=0.408552 (51301/125568, TOPMED)
G=0.369914 (43897/118668, ExAC) (+ 13 more)
G=0.38586 (12065/31268, GnomAD)
G=0.37864 (4911/12970, GO-ESP)
G=0.36382 (4066/11176, ALFA Project)
G=0.4325 (2166/5008, 1000G)
G=0.3009 (1348/4480, Estonian)
G=0.4567 (1338/2930, KOREAN)
G=0.4487 (822/1832, Korea1K)
G=0.341 (340/998, GoNL)
G=0.403 (242/600, NorthernSweden)
G=0.086 (46/534, MGP)
T=0.284 (112/394, SGDP_PRJ)
G=0.481 (104/216, Qatari)
T=0.42 (10/24, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Intron 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.87961150T>G
GRCh37.p13 chr 10 NC_000010.10:g.89720907T>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.102712T>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.176939T>G
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+32T>G N/A Intron Variant
PTEN transcript variant 1 NM_001304717.5:c.1546+32T…

NM_001304717.5:c.1546+32T>G

N/A Intron Variant
PTEN transcript variant 2 NM_001304718.2:c.435+32T>G N/A Intron 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: 98717 )
ClinVar Accession Disease Names Clinical Significance
RCV000078603.6 not specified Benign
RCV000710294.1 PTEN hamartoma tumor syndrome 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 27950 T=0.63553 G=0.36447
European Sub 20396 T=0.66155 G=0.33845
African Sub 3554 T=0.5124 G=0.4876
African Others Sub 122 T=0.484 G=0.516
African American Sub 3432 T=0.5134 G=0.4866
Asian Sub 168 T=0.512 G=0.488
East Asian Sub 112 T=0.491 G=0.509
Other Asian Sub 56 T=0.55 G=0.45
Latin American 1 Sub 146 T=0.568 G=0.432
Latin American 2 Sub 610 T=0.556 G=0.444
South Asian Sub 98 T=0.68 G=0.32
Other Sub 2978 T=0.6293 G=0.3707


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 248338 T=0.626694 G=0.373306
gnomAD - Exomes European Sub 133730 T=0.663359 G=0.336641
gnomAD - Exomes Asian Sub 48902 T=0.62382 G=0.37618
gnomAD - Exomes American Sub 34434 T=0.54257 G=0.45743
gnomAD - Exomes African Sub 15230 T=0.50190 G=0.49810
gnomAD - Exomes Ashkenazi Jewish Sub 10010 T=0.62867 G=0.37133
gnomAD - Exomes Other Sub 6032 T=0.6291 G=0.3709
TopMed Global Study-wide 125568 T=0.591448 G=0.408552
ExAC Global Study-wide 118668 T=0.630086 G=0.369914
ExAC Europe Sub 71810 T=0.66126 G=0.33874
ExAC Asian Sub 25032 T=0.62979 G=0.37021
ExAC American Sub 11444 T=0.54500 G=0.45500
ExAC African Sub 9490 T=0.4993 G=0.5007
ExAC Other Sub 892 T=0.612 G=0.388
gnomAD - Genomes Global Study-wide 31268 T=0.61414 G=0.38586
gnomAD - Genomes European Sub 18826 T=0.67486 G=0.32514
gnomAD - Genomes African Sub 8674 T=0.5024 G=0.4976
gnomAD - Genomes East Asian Sub 1554 T=0.5129 G=0.4871
gnomAD - Genomes Other Sub 1086 T=0.6372 G=0.3628
gnomAD - Genomes American Sub 840 T=0.570 G=0.430
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.597 G=0.403
GO Exome Sequencing Project Global Study-wide 12970 T=0.62136 G=0.37864
GO Exome Sequencing Project European American Sub 8584 T=0.6726 G=0.3274
GO Exome Sequencing Project African American Sub 4386 T=0.5210 G=0.4790
ALFA Total Global 11176 T=0.63618 G=0.36382
ALFA European Sub 8134 T=0.6416 G=0.3584
ALFA Other Sub 2302 T=0.6368 G=0.3632
ALFA African Sub 676 T=0.577 G=0.423
ALFA Asian Sub 60 T=0.52 G=0.48
ALFA South Asian Sub 4 T=1.0 G=0.0
ALFA Latin American 1 Sub 0 T=0 G=0
ALFA Latin American 2 Sub 0 T=0 G=0
1000Genomes Global Study-wide 5008 T=0.5675 G=0.4325
1000Genomes African Sub 1322 T=0.4743 G=0.5257
1000Genomes East Asian Sub 1008 T=0.4960 G=0.5040
1000Genomes Europe Sub 1006 T=0.6292 G=0.3708
1000Genomes South Asian Sub 978 T=0.710 G=0.290
1000Genomes American Sub 694 T=0.559 G=0.441
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6991 G=0.3009
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5433 G=0.4567
Korean Genome Project KOREAN Study-wide 1832 T=0.5513 G=0.4487
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.659 G=0.341
Northern Sweden ACPOP Study-wide 600 T=0.597 G=0.403
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.914 G=0.086
SGDP_PRJ Global Study-wide 394 T=0.284 G=0.716
Qatari Global Study-wide 216 T=0.519 G=0.481
Siberian Global Study-wide 24 T=0.42 G=0.58
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 T= G
GRCh38.p12 chr 10 NC_000010.11:g.87961150= NC_000010.11:g.87961150T>G
GRCh37.p13 chr 10 NC_000010.10:g.89720907= NC_000010.10:g.89720907T>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.102712= NG_007466.2:g.102712T>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.176939= NW_013171807.1:g.176939T>G
PTEN transcript NM_000314.4:c.1026+32= NM_000314.4:c.1026+32T>G
PTEN transcript variant 1 NM_000314.6:c.1026+32= NM_000314.6:c.1026+32T>G
PTEN transcript variant 1 NM_000314.8:c.1026+32= NM_000314.8:c.1026+32T>G
PTEN transcript variant 1 NM_001304717.2:c.1545+32= NM_001304717.2:c.1545+32T>G
PTEN transcript variant 1 NM_001304717.5:c.1546+32= NM_001304717.5:c.1546+32T>G
PTEN transcript variant 2 NM_001304718.1:c.435+32= NM_001304718.1:c.435+32T>G
PTEN transcript variant 2 NM_001304718.2:c.435+32= NM_001304718.2:c.435+32T>G
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#.

63 SubSNP, 16 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss726920 Aug 11, 2000 (83)
2 KWOK ss1038069 Oct 04, 2000 (86)
3 WI_SSAHASNP ss14421886 Dec 05, 2003 (119)
4 IMCJ-GDT ss28503393 Sep 24, 2004 (126)
5 EGP_SNPS ss38349835 Mar 11, 2006 (126)
6 ABI ss39819690 Mar 11, 2006 (126)
7 SI_EXO ss61707552 Oct 16, 2006 (127)
8 BCMHGSC_JDW ss88301789 Mar 23, 2008 (129)
9 BGI ss102899712 Dec 01, 2009 (131)
10 ILLUMINA-UK ss119257676 Feb 15, 2009 (130)
11 GMI ss155345523 Dec 01, 2009 (131)
12 ENSEMBL ss161369396 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss170682315 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss174678699 Jul 04, 2010 (132)
15 BUSHMAN ss201828340 Jul 04, 2010 (132)
16 1000GENOMES ss224860489 Jul 14, 2010 (132)
17 1000GENOMES ss235274496 Jul 15, 2010 (132)
18 1000GENOMES ss241961752 Jul 15, 2010 (132)
19 BL ss254496985 May 09, 2011 (134)
20 GMI ss280714853 May 04, 2012 (137)
21 GMI ss286235662 Apr 25, 2013 (138)
22 PJP ss290890284 May 09, 2011 (134)
23 ILLUMINA ss535728623 Sep 08, 2015 (146)
24 TISHKOFF ss562115210 Apr 25, 2013 (138)
25 SSMP ss657123241 Apr 25, 2013 (138)
26 NHLBI-ESP ss712956823 Apr 25, 2013 (138)
27 EVA-GONL ss987754561 Aug 21, 2014 (142)
28 1000GENOMES ss1338439511 Aug 21, 2014 (142)
29 DDI ss1426397486 Apr 01, 2015 (144)
30 EVA_EXAC ss1689987395 Apr 01, 2015 (144)
31 EVA_MGP ss1711264006 Apr 01, 2015 (144)
32 HAMMER_LAB ss1806500742 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1931122841 Feb 12, 2016 (147)
34 GENOMED ss1967189165 Jul 19, 2016 (147)
35 ILLUMINA ss2095015806 Dec 20, 2016 (150)
36 USC_VALOUEV ss2154564557 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2176768527 Dec 20, 2016 (150)
38 TOPMED ss2339871986 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2627613665 Nov 08, 2017 (151)
40 GRF ss2698815874 Nov 08, 2017 (151)
41 GNOMAD ss2738382764 Nov 08, 2017 (151)
42 GNOMAD ss2748430680 Nov 08, 2017 (151)
43 GNOMAD ss2891608120 Nov 08, 2017 (151)
44 SWEGEN ss3006889924 Nov 08, 2017 (151)
45 TOPMED ss3126321628 Nov 08, 2017 (151)
46 CSHL ss3349240473 Nov 08, 2017 (151)
47 ILLUMINA ss3626499444 Oct 12, 2018 (152)
48 OMUKHERJEE_ADBS ss3646412920 Oct 12, 2018 (152)
49 ILLUMINA ss3651618574 Oct 12, 2018 (152)
50 EGCUT_WGS ss3674299694 Jul 13, 2019 (153)
51 ACPOP ss3737543936 Jul 13, 2019 (153)
52 EVA ss3748412255 Jul 13, 2019 (153)
53 PACBIO ss3786744149 Jul 13, 2019 (153)
54 PACBIO ss3791913893 Jul 13, 2019 (153)
55 PACBIO ss3796796000 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3813779671 Jul 13, 2019 (153)
57 EVA ss3824535897 Apr 26, 2020 (154)
58 EVA ss3825779610 Apr 26, 2020 (154)
59 EVA ss3839667021 Apr 26, 2020 (154)
60 EVA ss3845140439 Apr 26, 2020 (154)
61 SGDP_PRJ ss3874733698 Apr 26, 2020 (154)
62 KRGDB ss3922849605 Apr 26, 2020 (154)
63 KOGIC ss3968370635 Apr 26, 2020 (154)
64 1000Genomes NC_000010.10 - 89720907 Oct 12, 2018 (152)
65 Genetic variation in the Estonian population NC_000010.10 - 89720907 Oct 12, 2018 (152)
66 ExAC NC_000010.10 - 89720907 Oct 12, 2018 (152)
67 gnomAD - Genomes NC_000010.10 - 89720907 Jul 13, 2019 (153)
68 gnomAD - Exomes NC_000010.10 - 89720907 Jul 13, 2019 (153)
69 GO Exome Sequencing Project NC_000010.10 - 89720907 Oct 12, 2018 (152)
70 Genome of the Netherlands Release 5 NC_000010.10 - 89720907 Apr 26, 2020 (154)
71 KOREAN population from KRGDB NC_000010.10 - 89720907 Apr 26, 2020 (154)
72 Korean Genome Project NC_000010.11 - 87961150 Apr 26, 2020 (154)
73 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 89720907 Apr 26, 2020 (154)
74 Northern Sweden NC_000010.10 - 89720907 Jul 13, 2019 (153)
75 Qatari NC_000010.10 - 89720907 Apr 26, 2020 (154)
76 SGDP_PRJ NC_000010.10 - 89720907 Apr 26, 2020 (154)
77 Siberian NC_000010.10 - 89720907 Apr 26, 2020 (154)
78 TopMed NC_000010.11 - 87961150 Oct 12, 2018 (152)
79 dbGaP Population Frequency Project NC_000010.11 - 87961150 Apr 26, 2020 (154)
80 ClinVar RCV000078603.6 Apr 26, 2020 (154)
81 ClinVar RCV000710294.1 Jul 13, 2019 (153)
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)
rs17849091 Mar 11, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss88301789, ss119257676, ss170682315, ss174678699, ss201828340, ss254496985, ss280714853, ss286235662, ss290890284 NC_000010.9:89710886:T:G NC_000010.11:87961149:T:G (self)
50863932, 20037942, 214825, 138962545, 7581679, 993583, 12590557, 30026999, 379766, 10828801, 13164771, 26750678, 7080911, ss224860489, ss235274496, ss241961752, ss535728623, ss562115210, ss657123241, ss712956823, ss987754561, ss1338439511, ss1426397486, ss1689987395, ss1711264006, ss1806500742, ss1931122841, ss1967189165, ss2095015806, ss2154564557, ss2339871986, ss2627613665, ss2698815874, ss2738382764, ss2748430680, ss2891608120, ss3006889924, ss3349240473, ss3626499444, ss3646412920, ss3651618574, ss3674299694, ss3737543936, ss3748412255, ss3786744149, ss3791913893, ss3796796000, ss3824535897, ss3825779610, ss3839667021, ss3874733698, ss3922849605 NC_000010.10:89720906:T:G NC_000010.11:87961149:T:G (self)
RCV000078603.6, RCV000710294.1, 24748636, 48130804, 425480585, ss2176768527, ss3126321628, ss3813779671, ss3845140439, ss3968370635 NC_000010.11:87961149:T:G NC_000010.11:87961149:T:G (self)
ss61707552 NT_030059.12:8469422:T:G NC_000010.11:87961149:T:G (self)
ss726920, ss1038069, ss14421886, ss28503393, ss38349835, ss39819690, ss102899712, ss155345523, ss161369396 NT_030059.13:40525370:T:G NC_000010.11:87961149:T: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 rs555895
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
18805939 Functional genetic polymorphisms and female reproductive disorders: part II--endometriosis. Tempfer CB et al. 2009 Human reproduction update
23068025 Association of PTEN genetic polymorphisms with atherosclerotic cerebral infarction in the Han Chinese population. Yuan M et al. 2012 Journal of clinical neuroscience
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
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
26541596 Association of genetic polymorphisms in PTEN and additional gene-gene interaction with risk of esophageal squamous cell carcinoma in Chinese Han population. Xu X et al. 2016 Diseases of the esophagus
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