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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
chr10:87864984 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
T=0.013554 (1702/125568, TOPMED)
T=0.02244 (1766/78698, PAGE_STUDY)
T=0.01385 (435/31404, GnomAD) (+ 7 more)
T=0.0158 (79/5008, 1000G)
T=0.0003 (1/3854, ALSPAC)
T=0.0021 (8/3778, ALFA Project)
T=0.0000 (0/3708, TWINSUK)
T=0.019 (4/216, Qatari)
C=0.5 (4/8, SGDP_PRJ)
T=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Intron Variant
KLLN : 2KB Upstream 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.87864984C>G
GRCh38.p12 chr 10 NC_000010.11:g.87864984C>T
GRCh37.p13 chr 10 NC_000010.10:g.89624741C>G
GRCh37.p13 chr 10 NC_000010.10:g.89624741C>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.6546C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.6546C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.3454G>C
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.3454G>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.80807C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.80807C>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.79+436C>G N/A Intron Variant
PTEN transcript variant 1 NM_001304717.5:c.599+436C…


N/A Intron Variant
PTEN transcript variant 2 NM_001304718.2:c.-627+436…


N/A Intron 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

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: 225702 )
ClinVar Accession Disease Names Clinical Significance
RCV000209749.1 Hereditary cancer-predisposing 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 25984 C=0.99784 G=0.00000, T=0.00216
European Sub 20206 C=0.99951 G=0.00000, T=0.00049
African Sub 3348 C=0.9895 G=0.0000, T=0.0105
African Others Sub 110 C=1.000 G=0.000, T=0.000
African American Sub 3238 C=0.9892 G=0.0000, T=0.0108
Asian Sub 162 C=1.000 G=0.000, T=0.000
East Asian Sub 134 C=1.000 G=0.000, T=0.000
Other Asian Sub 28 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 166 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 696 C=0.999 G=0.000, T=0.001
South Asian Sub 118 C=1.000 G=0.000, T=0.000
Other Sub 1288 C=0.9922 G=0.0000, T=0.0078


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=0.986430 G=0.000016, T=0.013554
The PAGE Study Global Study-wide 78698 C=0.97756 T=0.02244
The PAGE Study AfricanAmerican Sub 32514 C=0.95442 T=0.04558
The PAGE Study Mexican Sub 10810 C=0.99713 T=0.00287
The PAGE Study Asian Sub 8318 C=0.9999 T=0.0001
The PAGE Study PuertoRican Sub 7916 C=0.9876 T=0.0124
The PAGE Study NativeHawaiian Sub 4534 C=0.9996 T=0.0004
The PAGE Study Cuban Sub 4230 C=0.9901 T=0.0099
The PAGE Study Dominican Sub 3828 C=0.9799 T=0.0201
The PAGE Study CentralAmerican Sub 2450 C=0.9922 T=0.0078
The PAGE Study SouthAmerican Sub 1982 C=0.9955 T=0.0045
The PAGE Study NativeAmerican Sub 1260 C=0.9960 T=0.0040
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 31404 C=0.98615 T=0.01385
gnomAD - Genomes European Sub 18908 C=0.99979 T=0.00021
gnomAD - Genomes African Sub 8710 C=0.9510 T=0.0490
gnomAD - Genomes East Asian Sub 1560 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1088 C=0.9991 T=0.0009
gnomAD - Genomes American Sub 848 C=0.996 T=0.004
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9842 T=0.0158
1000Genomes African Sub 1322 C=0.9433 T=0.0567
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9990 T=0.0010
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.996 T=0.004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
ALFA Total Global 3778 C=0.9979 G=0.0000, T=0.0021
ALFA European Sub 3356 C=0.9997 G=0.0000, T=0.0003
ALFA Other Sub 202 C=0.985 G=0.000, T=0.015
ALFA African Sub 152 C=0.974 G=0.000, T=0.026
ALFA Asian Sub 46 C=1.00 G=0.00, T=0.00
ALFA Latin American 2 Sub 10 C=1.0 G=0.0, T=0.0
ALFA South Asian Sub 10 C=1.0 G=0.0, T=0.0
ALFA Latin American 1 Sub 2 C=1.0 G=0.0, T=0.0
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
Qatari Global Study-wide 216 C=0.981 T=0.019
SGDP_PRJ Global Study-wide 8 C=0.5 T=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= G T
GRCh38.p12 chr 10 NC_000010.11:g.87864984= NC_000010.11:g.87864984C>G NC_000010.11:g.87864984C>T
GRCh37.p13 chr 10 NC_000010.10:g.89624741= NC_000010.10:g.89624741C>G NC_000010.10:g.89624741C>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.6546= NG_007466.2:g.6546C>G NG_007466.2:g.6546C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.3454= NG_033079.1:g.3454G>C NG_033079.1:g.3454G>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.80807= NW_013171807.1:g.80807C>G NW_013171807.1:g.80807C>T
PTEN transcript NM_000314.4:c.79+436= NM_000314.4:c.79+436C>G NM_000314.4:c.79+436C>T
PTEN transcript variant 1 NM_000314.6:c.79+436= NM_000314.6:c.79+436C>G NM_000314.6:c.79+436C>T
PTEN transcript variant 1 NM_000314.8:c.79+436= NM_000314.8:c.79+436C>G NM_000314.8:c.79+436C>T
PTEN transcript variant 1 NM_001304717.2:c.598+436= NM_001304717.2:c.598+436C>G NM_001304717.2:c.598+436C>T
PTEN transcript variant 1 NM_001304717.5:c.599+436= NM_001304717.5:c.599+436C>G NM_001304717.5:c.599+436C>T
PTEN transcript variant 2 NM_001304718.1:c.-627+436= NM_001304718.1:c.-627+436C>G NM_001304718.1:c.-627+436C>T
PTEN transcript variant 2 NM_001304718.2:c.-627+436= NM_001304718.2:c.-627+436C>G NM_001304718.2:c.-627+436C>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#.

27 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss38349672 Mar 13, 2006 (126)
2 1000GENOMES ss224860318 Jul 14, 2010 (132)
3 ILLUMINA ss482398639 May 04, 2012 (137)
4 ILLUMINA ss482681021 May 04, 2012 (137)
5 ILLUMINA ss534631987 Sep 08, 2015 (146)
6 ILLUMINA ss779999638 Sep 08, 2015 (146)
7 ILLUMINA ss781748341 Sep 08, 2015 (146)
8 ILLUMINA ss835479286 Sep 08, 2015 (146)
9 1000GENOMES ss1338437082 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1625093252 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1668087285 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1931122232 Feb 12, 2016 (147)
13 ILLUMINA ss1959281022 Feb 12, 2016 (147)
14 HUMAN_LONGEVITY ss2176762912 Dec 20, 2016 (150)
15 TOPMED ss2339866248 Dec 20, 2016 (150)
16 ILLUMINA ss2632742254 Nov 08, 2017 (151)
17 GNOMAD ss2891600765 Nov 08, 2017 (151)
18 ILLUMINA ss3021260731 Nov 08, 2017 (151)
19 TOPMED ss3126304457 Nov 08, 2017 (151)
20 TOPMED ss3126304458 Nov 08, 2017 (151)
21 ILLUMINA ss3626499342 Oct 12, 2018 (152)
22 ILLUMINA ss3630766060 Oct 12, 2018 (152)
23 ILLUMINA ss3641691700 Oct 12, 2018 (152)
24 ILLUMINA ss3651618442 Oct 12, 2018 (152)
25 ILLUMINA ss3725175697 Jul 13, 2019 (153)
26 PAGE_CC ss3771572617 Jul 13, 2019 (153)
27 SGDP_PRJ ss3874732517 Apr 26, 2020 (154)
28 1000Genomes NC_000010.10 - 89624741 Oct 12, 2018 (152)
29 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89624741 Oct 12, 2018 (152)
30 gnomAD - Genomes NC_000010.10 - 89624741 Jul 13, 2019 (153)
31 The PAGE Study NC_000010.11 - 87864984 Jul 13, 2019 (153)
32 Qatari NC_000010.10 - 89624741 Apr 26, 2020 (154)
33 SGDP_PRJ NC_000010.10 - 89624741 Apr 26, 2020 (154)
34 TopMed NC_000010.11 - 87864984 Oct 12, 2018 (152)
35 UK 10K study - Twins NC_000010.10 - 89624741 Oct 12, 2018 (152)
36 dbGaP Population Frequency Project NC_000010.11 - 87864984 Apr 26, 2020 (154)
37 ClinVar RCV000209749.1 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
48115657, 192229948, ss3126304457 NC_000010.11:87864983:C:G NC_000010.11:87864983:C:G (self)
ss482681021 NC_000010.9:89614720:C:T NC_000010.11:87864983:C:T (self)
50861383, 28232205, 138955148, 13164162, 26749497, 28232205, ss224860318, ss482398639, ss534631987, ss779999638, ss781748341, ss835479286, ss1338437082, ss1625093252, ss1668087285, ss1931122232, ss1959281022, ss2339866248, ss2632742254, ss2891600765, ss3021260731, ss3626499342, ss3630766060, ss3641691700, ss3651618442, ss3874732517 NC_000010.10:89624740:C:T NC_000010.11:87864983:C:T (self)
RCV000209749.1, 794086, 48115657, 192229948, ss2176762912, ss3126304458, ss3725175697, ss3771572617 NC_000010.11:87864983:C:T NC_000010.11:87864983:C:T (self)
ss38349672 NT_030059.13:40429204:C:T NC_000010.11:87864983:C: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 rs34370865


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