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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.


Current Build 154

Released April 21, 2020

Homo sapiens
chr10:87967037 (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.

C>A / C>G
Variation Type
SNV Single Nucleotide Variation
A=0.010958 (1376/125568, TOPMED)
A=0.01125 (350/31102, GnomAD)
A=0.0010 (10/9982, ALFA Project) (+ 4 more)
A=0.0110 (55/5008, 1000G)
A=0.014 (3/216, Qatari)
C=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
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.87967037C>A
GRCh38.p12 chr 10 NC_000010.11:g.87967037C>G
GRCh37.p13 chr 10 NC_000010.10:g.89726794C>A
GRCh37.p13 chr 10 NC_000010.10:g.89726794C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.108599C>A
PTEN RefSeqGene (LRG_311) NG_007466.2:g.108599C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.182826C>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.182826C>G
Gene: PTEN, phosphatase and tensin homolog (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 2 NM_001304718.2:c.*1565= N/A 3 Prime UTR Variant
PTEN transcript variant 1 NM_001304717.5:c.*1565= N/A 3 Prime UTR Variant
PTEN transcript variant 1 NM_000314.8:c.*1565= 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: A (allele ID: 317146 )
ClinVar Accession Disease Names Clinical Significance
RCV000390847.1 PTEN hamartoma tumor syndrome Likely-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 32102 C=0.99639 A=0.00361
European Sub 26378 C=0.99992 A=0.00008
African Sub 3168 C=0.9675 A=0.0325
African Others Sub 124 C=0.944 A=0.056
African American Sub 3044 C=0.9685 A=0.0315
Asian Sub 128 C=1.000 A=0.000
East Asian Sub 100 C=1.00 A=0.00
Other Asian Sub 28 C=1.00 A=0.00
Latin American 1 Sub 168 C=0.994 A=0.006
Latin American 2 Sub 700 C=0.999 A=0.001
South Asian Sub 114 C=1.000 A=0.000
Other Sub 1446 C=0.9938 A=0.0062


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 C=0.989042 A=0.010958
gnomAD - Genomes Global Study-wide 31102 C=0.98875 A=0.01125
gnomAD - Genomes European Sub 18690 C=0.99989 A=0.00011
gnomAD - Genomes African Sub 8664 C=0.9602 A=0.0398
gnomAD - Genomes East Asian Sub 1560 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1068 C=0.9991 A=0.0009
gnomAD - Genomes American Sub 832 C=0.998 A=0.002
gnomAD - Genomes Ashkenazi Jewish Sub 288 C=1.000 A=0.000
ALFA Total Global 9982 C=0.9990 A=0.0010
ALFA European Sub 9398 C=0.9999 A=0.0001
ALFA Other Sub 394 C=0.997 A=0.003
ALFA African Sub 160 C=0.950 A=0.050
ALFA Latin American 2 Sub 12 C=1.00 A=0.00
ALFA Asian Sub 12 C=1.00 A=0.00
ALFA South Asian Sub 4 C=1.0 A=0.0
ALFA Latin American 1 Sub 2 C=1.0 A=0.0
1000Genomes Global Study-wide 5008 C=0.9890 A=0.0110
1000Genomes African Sub 1322 C=0.9607 A=0.0393
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=0.9990 A=0.0010
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=0.997 A=0.003
Qatari Global Study-wide 216 C=0.986 A=0.014
SGDP_PRJ Global Study-wide 6 C=0.5 A=0.5

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= A G
GRCh38.p12 chr 10 NC_000010.11:g.87967037= NC_000010.11:g.87967037C>A NC_000010.11:g.87967037C>G
GRCh37.p13 chr 10 NC_000010.10:g.89726794= NC_000010.10:g.89726794C>A NC_000010.10:g.89726794C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.108599= NG_007466.2:g.108599C>A NG_007466.2:g.108599C>G
PTEN transcript variant 1 NM_000314.8:c.*1565= NM_000314.8:c.*1565C>A NM_000314.8:c.*1565C>G
PTEN transcript variant 1 NM_000314.7:c.*1565= NM_000314.7:c.*1565C>A NM_000314.7:c.*1565C>G
PTEN transcript variant 1 NM_000314.6:c.*1565= NM_000314.6:c.*1565C>A NM_000314.6:c.*1565C>G
PTEN transcript NM_000314.4:c.*1565= NM_000314.4:c.*1565C>A NM_000314.4:c.*1565C>G
PTEN transcript variant 1 NM_001304717.5:c.*1565= NM_001304717.5:c.*1565C>A NM_001304717.5:c.*1565C>G
PTEN transcript variant 1 NM_001304717.4:c.*1565= NM_001304717.4:c.*1565C>A NM_001304717.4:c.*1565C>G
PTEN transcript variant 1 NM_001304717.3:c.*1565= NM_001304717.3:c.*1565C>A NM_001304717.3:c.*1565C>G
PTEN transcript variant 1 NM_001304717.2:c.*1565= NM_001304717.2:c.*1565C>A NM_001304717.2:c.*1565C>G
PTEN transcript variant 2 NM_001304718.2:c.*1565= NM_001304718.2:c.*1565C>A NM_001304718.2:c.*1565C>G
PTEN transcript variant 2 NM_001304718.1:c.*1565= NM_001304718.1:c.*1565C>A NM_001304718.1:c.*1565C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.182826= NW_013171807.1:g.182826C>A NW_013171807.1:g.182826C>G

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#.

23 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss38349854 Mar 13, 2006 (126)
2 ILLUMINA ss169064370 Jul 04, 2010 (132)
3 BUSHMAN ss201828360 Jul 04, 2010 (132)
4 1000GENOMES ss224860501 Jul 14, 2010 (132)
5 ILLUMINA ss482358847 May 04, 2012 (137)
6 ILLUMINA ss482681128 May 04, 2012 (137)
7 ILLUMINA ss534614523 Sep 08, 2015 (146)
8 ILLUMINA ss779360887 Sep 08, 2015 (146)
9 ILLUMINA ss781735215 Sep 08, 2015 (146)
10 ILLUMINA ss834829076 Sep 08, 2015 (146)
11 1000GENOMES ss1338439633 Aug 21, 2014 (142)
12 WEILL_CORNELL_DGM ss1931122880 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2176768803 Dec 20, 2016 (150)
14 TOPMED ss2339872297 Dec 20, 2016 (150)
15 ILLUMINA ss2632742303 Nov 08, 2017 (151)
16 GNOMAD ss2891608572 Nov 08, 2017 (151)
17 AFFY ss2985567113 Nov 08, 2017 (151)
18 TOPMED ss3126322772 Nov 08, 2017 (151)
19 ILLUMINA ss3626499457 Oct 12, 2018 (152)
20 ILLUMINA ss3630766106 Oct 12, 2018 (152)
21 ILLUMINA ss3637864281 Oct 12, 2018 (152)
22 ILLUMINA ss3653689215 Oct 12, 2018 (152)
23 SGDP_PRJ ss3874733775 Apr 26, 2020 (154)
24 1000Genomes NC_000010.10 - 89726794 Oct 12, 2018 (152)
25 gnomAD - Genomes NC_000010.10 - 89726794 Jul 13, 2019 (153)
26 Qatari NC_000010.10 - 89726794 Apr 26, 2020 (154)
27 SGDP_PRJ NC_000010.10 - 89726794 Apr 26, 2020 (154)
28 TopMed NC_000010.11 - 87967037 Oct 12, 2018 (152)
29 dbGaP Population Frequency Project NC_000010.11 - 87967037 Apr 26, 2020 (154)
30 ClinVar RCV000390847.1 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).

Associated ID History Updated (Build)
rs386453289 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss482681128 NC_000010.9:89716773:C:A NC_000010.11:87967036:C:A (self)
50864060, 138963033, 13164810, 26750755, ss224860501, ss482358847, ss534614523, ss779360887, ss781735215, ss834829076, ss1338439633, ss1931122880, ss2339872297, ss2632742303, ss2891608572, ss2985567113, ss3626499457, ss3630766106, ss3637864281, ss3653689215, ss3874733775 NC_000010.10:89726793:C:A NC_000010.11:87967036:C:A (self)
RCV000390847.1, 48131635, 863007616, ss2176768803, ss3126322772 NC_000010.11:87967036:C:A NC_000010.11:87967036:C:A (self)
ss38349854, ss169064370 NT_030059.13:40531257:C:A NC_000010.11:87967036:C:A (self)
ss201828360 NC_000010.9:89716773:C:G NC_000010.11:87967036:C:G (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 rs34140758


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