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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
chr10:87932979 (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
G=0.000450 (112/249024, GnomAD_exome)
G=0.001752 (220/125568, TOPMED)
G=0.000556 (66/118672, ExAC) (+ 4 more)
G=0.00198 (62/31374, GnomAD)
G=0.00177 (23/12992, GO-ESP)
G=0.00018 (2/11176, ALFA Project)
G=0.0016 (8/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Intron 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.87932979T>G
GRCh37.p13 chr 10 NC_000010.10:g.89692736T>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.74541T>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.148771T>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.254-34T>G N/A Intron Variant
PTEN transcript variant 1 NM_001304717.5:c.774-34T>G N/A Intron Variant
PTEN transcript variant 2 NM_001304718.2:c.-497-34T…


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: G (allele ID: 790998 )
ClinVar Accession Disease Names Clinical Significance
RCV000988414.1 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 23408 T=0.99876 G=0.00124
European Sub 15886 T=1.00000 G=0.00000
African Sub 3540 T=0.9924 G=0.0076
African Others Sub 122 T=0.992 G=0.008
African American Sub 3418 T=0.9924 G=0.0076
Asian Sub 168 T=1.000 G=0.000
East Asian Sub 112 T=1.000 G=0.000
Other Asian Sub 56 T=1.00 G=0.00
Latin American 1 Sub 146 T=1.000 G=0.000
Latin American 2 Sub 610 T=1.000 G=0.000
South Asian Sub 98 T=1.00 G=0.00
Other Sub 2960 T=0.9993 G=0.0007


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
gnomAD - Exomes Global Study-wide 249024 T=0.999550 G=0.000450
gnomAD - Exomes European Sub 134160 T=0.999993 G=0.000007
gnomAD - Exomes Asian Sub 48788 T=0.99998 G=0.00002
gnomAD - Exomes American Sub 34396 T=0.99980 G=0.00020
gnomAD - Exomes African Sub 15598 T=0.99352 G=0.00648
gnomAD - Exomes Ashkenazi Jewish Sub 10038 T=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6044 T=0.9997 G=0.0003
TopMed Global Study-wide 125568 T=0.998248 G=0.001752
ExAC Global Study-wide 118672 T=0.999444 G=0.000556
ExAC Europe Sub 71990 T=1.00000 G=0.00000
ExAC Asian Sub 24706 T=1.00000 G=0.00000
ExAC American Sub 11412 T=0.99982 G=0.00018
ExAC African Sub 9674 T=0.9935 G=0.0065
ExAC Other Sub 890 T=0.999 G=0.001
gnomAD - Genomes Global Study-wide 31374 T=0.99802 G=0.00198
gnomAD - Genomes European Sub 18886 T=1.00000 G=0.00000
gnomAD - Genomes African Sub 8708 T=0.9931 G=0.0069
gnomAD - Genomes East Asian Sub 1560 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 1086 T=0.9991 G=0.0009
gnomAD - Genomes American Sub 844 T=0.999 G=0.001
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 12992 T=0.99823 G=0.00177
GO Exome Sequencing Project European American Sub 8590 T=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4402 T=0.9948 G=0.0052
ALFA Total Global 11176 T=0.99982 G=0.00018
ALFA European Sub 8134 T=1.0000 G=0.0000
ALFA Other Sub 2302 T=1.0000 G=0.0000
ALFA African Sub 676 T=0.997 G=0.003
ALFA Asian Sub 60 T=1.00 G=0.00
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=0.9984 G=0.0016
1000Genomes African Sub 1322 T=0.9939 G=0.0061
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=1.0000 G=0.0000
1000Genomes South Asian Sub 978 T=1.000 G=0.000
1000Genomes American Sub 694 T=1.000 G=0.000

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.87932979= NC_000010.11:g.87932979T>G
GRCh37.p13 chr 10 NC_000010.10:g.89692736= NC_000010.10:g.89692736T>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.74541= NG_007466.2:g.74541T>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.148771= NW_013171807.1:g.148771T>G
PTEN transcript NM_000314.4:c.254-34= NM_000314.4:c.254-34T>G
PTEN transcript variant 1 NM_000314.6:c.254-34= NM_000314.6:c.254-34T>G
PTEN transcript variant 1 NM_000314.8:c.254-34= NM_000314.8:c.254-34T>G
PTEN transcript variant 1 NM_001304717.2:c.773-34= NM_001304717.2:c.773-34T>G
PTEN transcript variant 1 NM_001304717.5:c.774-34= NM_001304717.5:c.774-34T>G
PTEN transcript variant 2 NM_001304718.1:c.-497-34= NM_001304718.1:c.-497-34T>G
PTEN transcript variant 2 NM_001304718.2:c.-497-34= NM_001304718.2:c.-497-34T>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#.

12 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SNP500CANCER ss48296536 Mar 13, 2006 (126)
2 1000GENOMES ss461790945 Sep 17, 2011 (135)
3 NHLBI-ESP ss712956811 Apr 25, 2013 (138)
4 1000GENOMES ss1338438818 Aug 21, 2014 (142)
5 EVA_EXAC ss1689987270 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2176766941 Dec 20, 2016 (150)
7 TOPMED ss2339870373 Dec 20, 2016 (150)
8 GNOMAD ss2738382582 Nov 08, 2017 (151)
9 GNOMAD ss2748430631 Nov 08, 2017 (151)
10 GNOMAD ss2891606005 Nov 08, 2017 (151)
11 TOPMED ss3126316755 Nov 08, 2017 (151)
12 EVA ss3824535879 Apr 26, 2020 (154)
13 1000Genomes NC_000010.10 - 89692736 Oct 12, 2018 (152)
14 ExAC NC_000010.10 - 89692736 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000010.10 - 89692736 Jul 13, 2019 (153)
16 gnomAD - Exomes NC_000010.10 - 89692736 Jul 13, 2019 (153)
17 GO Exome Sequencing Project NC_000010.10 - 89692736 Oct 12, 2018 (152)
18 TopMed NC_000010.11 - 87932979 Oct 12, 2018 (152)
19 dbGaP Population Frequency Project NC_000010.11 - 87932979 Apr 26, 2020 (154)
20 ClinVar RCV000988414.1 Apr 26, 2020 (154)

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
50863201, 214683, 138960427, 7581500, 993565, ss461790945, ss712956811, ss1338438818, ss1689987270, ss2339870373, ss2738382582, ss2748430631, ss2891606005, ss3824535879 NC_000010.10:89692735:T:G NC_000010.11:87932978:T:G (self)
RCV000988414.1, 48126616, 438375169, ss2176766941, ss3126316755 NC_000010.11:87932978:T:G NC_000010.11:87932978:T:G (self)
ss48296536 NT_030059.13:40497199:T:G NC_000010.11:87932978:T: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 rs34047313


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