Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.


Current Build 154

Released April 21, 2020

Homo sapiens
chr10:87968293 (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.

Variation Type
SNV Single Nucleotide Variation
T=0.000199 (25/125568, TOPMED)
T=0.00022 (7/31396, GnomAD)
T=0.0008 (3/3854, ALSPAC) (+ 3 more)
T=0.0003 (1/3708, TWINSUK)
T=0.0005 (1/2188, ALFA Project)
T=0.000 (0/316, HapMap)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : 3 Prime UTR Variant
0 citations
Genomic View
See rs on genome

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.87968293A>T
GRCh37.p13 chr 10 NC_000010.10:g.89728050A>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.109855A>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.184082A>T
Gene: PTEN, phosphatase and tensin homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 2 NM_001304718.2:c.*2821= N/A 3 Prime UTR Variant
PTEN transcript variant 1 NM_001304717.5:c.*2821= N/A 3 Prime UTR Variant
PTEN transcript variant 1 NM_000314.8:c.*2821= N/A 3 Prime UTR 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: 311571 )
ClinVar Accession Disease Names Clinical Significance
RCV000334034.1 PTEN hamartoma tumor syndrome Uncertain-Significance

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 14420 A=0.99965 T=0.00035
European Sub 9824 A=0.9995 T=0.0005
African Sub 2946 A=1.0000 T=0.0000
African Others Sub 114 A=1.000 T=0.000
African American Sub 2832 A=1.0000 T=0.0000
Asian Sub 112 A=1.000 T=0.000
East Asian Sub 86 A=1.00 T=0.00
Other Asian Sub 26 A=1.00 T=0.00
Latin American 1 Sub 146 A=1.000 T=0.000
Latin American 2 Sub 610 A=1.000 T=0.000
South Asian Sub 98 A=1.00 T=0.00
Other Sub 684 A=1.000 T=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.999801 T=0.000199
gnomAD - Genomes Global Study-wide 31396 A=0.99978 T=0.00022
gnomAD - Genomes European Sub 18898 A=0.99968 T=0.00032
gnomAD - Genomes African Sub 8716 A=0.9999 T=0.0001
gnomAD - Genomes East Asian Sub 1560 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1086 A=1.0000 T=0.0000
gnomAD - Genomes American Sub 846 A=1.000 T=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=1.000 T=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9992 T=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9997 T=0.0003
ALFA Total Global 2188 A=0.9995 T=0.0005
ALFA European Sub 2072 A=0.9995 T=0.0005
ALFA African Sub 82 A=1.00 T=0.00
ALFA Other Sub 26 A=1.00 T=0.00
ALFA South Asian Sub 4 A=1.0 T=0.0
ALFA Asian Sub 4 A=1.0 T=0.0
ALFA Latin American 1 Sub 0 A=0 T=0
ALFA Latin American 2 Sub 0 A=0 T=0
HapMap Global Study-wide 316 A=1.000 T=0.000
HapMap African Sub 120 A=1.000 T=0.000
HapMap American Sub 116 A=1.000 T=0.000
HapMap Asian Sub 80 A=1.00 T=0.00

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 A= T
GRCh38.p12 chr 10 NC_000010.11:g.87968293= NC_000010.11:g.87968293A>T
GRCh37.p13 chr 10 NC_000010.10:g.89728050= NC_000010.10:g.89728050A>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.109855= NG_007466.2:g.109855A>T
PTEN transcript variant 1 NM_000314.8:c.*2821= NM_000314.8:c.*2821A>T
PTEN transcript variant 1 NM_000314.7:c.*2821= NM_000314.7:c.*2821A>T
PTEN transcript variant 1 NM_000314.6:c.*2821= NM_000314.6:c.*2821A>T
PTEN transcript NM_000314.4:c.*2821= NM_000314.4:c.*2821A>T
PTEN transcript variant 1 NM_001304717.5:c.*2821= NM_001304717.5:c.*2821A>T
PTEN transcript variant 1 NM_001304717.4:c.*2821= NM_001304717.4:c.*2821A>T
PTEN transcript variant 1 NM_001304717.3:c.*2821= NM_001304717.3:c.*2821A>T
PTEN transcript variant 1 NM_001304717.2:c.*2821= NM_001304717.2:c.*2821A>T
PTEN transcript variant 2 NM_001304718.2:c.*2821= NM_001304718.2:c.*2821A>T
PTEN transcript variant 2 NM_001304718.1:c.*2821= NM_001304718.1:c.*2821A>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.184082= NW_013171807.1:g.184082A>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#.

13 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16463758 Feb 28, 2004 (120)
2 ABI ss38571490 Mar 13, 2006 (126)
3 ENSEMBL ss161369406 Dec 01, 2009 (131)
4 EVA_DECODE ss1597427376 Apr 01, 2015 (144)
5 EVA_UK10K_ALSPAC ss1625094836 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1668088869 Apr 01, 2015 (144)
7 HUMAN_LONGEVITY ss2176768876 Dec 20, 2016 (150)
8 TOPMED ss2339872372 Dec 20, 2016 (150)
9 ILLUMINA ss2635017559 Nov 08, 2017 (151)
10 GNOMAD ss2891608663 Nov 08, 2017 (151)
11 SWEGEN ss3006890006 Nov 08, 2017 (151)
12 TOPMED ss3126322998 Nov 08, 2017 (151)
13 EVA_DECODE ss3690370108 Jul 13, 2019 (153)
14 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89728050 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000010.10 - 89728050 Jul 13, 2019 (153)
16 HapMap NC_000010.11 - 87968293 Apr 26, 2020 (154)
17 TopMed NC_000010.11 - 87968293 Oct 12, 2018 (152)
18 UK 10K study - Twins NC_000010.10 - 89728050 Oct 12, 2018 (152)
19 dbGaP Population Frequency Project NC_000010.11 - 87968293 Apr 26, 2020 (154)
20 ClinVar RCV000334034.1 Oct 12, 2018 (152)

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
ss1597427376, ss2635017559 NC_000010.9:89718029:A:T NC_000010.11:87968292:A:T (self)
28233948, 138963125, 28233948, ss1625094836, ss1668088869, ss2339872372, ss2891608663, ss3006890006 NC_000010.10:89728049:A:T NC_000010.11:87968292:A:T (self)
RCV000334034.1, 457911, 48131842, 554080341, ss2176768876, ss3126322998, ss3690370108 NC_000010.11:87968292:A:T NC_000010.11:87968292:A:T (self)
ss16463758 NT_030059.11:8476565:A:T NC_000010.11:87968292:A:T (self)
ss38571490, ss161369406 NT_030059.13:40532513:A:T NC_000010.11:87968292:A:T (self)

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

No publications for rs11591427


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