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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.

rs17849090

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87957941 (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>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000008 (2/251452, GnomAD_exome)
C=0.000008 (1/121376, ExAC)
C=0.0000 (0/2922, KOREAN) (+ 1 more)
C=0.0000 (0/1154, ALFA Project)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Missense Variant
Publications
0 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.87957941T>C
GRCh38.p12 chr 10 NC_000010.11:g.87957941T>G
GRCh37.p13 chr 10 NC_000010.10:g.89717698T>C
GRCh37.p13 chr 10 NC_000010.10:g.89717698T>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.99503T>C
PTEN RefSeqGene (LRG_311) NG_007466.2:g.99503T>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.173730T>C
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.173730T>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.132T>C F [TTT] > F [TTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform 3 NP_001291647.1:p.Phe44= F (Phe) > F (Phe) Synonymous Variant
PTEN transcript variant 2 NM_001304718.2:c.132T>G F [TTT] > L [TTG] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform 3 NP_001291647.1:p.Phe44Leu F (Phe) > L (Leu) Missense Variant
PTEN transcript variant 1 NM_001304717.5:c.1242T>C F [TTT] > F [TTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Phe414= F (Phe) > F (Phe) Synonymous Variant
PTEN transcript variant 1 NM_001304717.5:c.1242T>G F [TTT] > L [TTG] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Phe414Leu F (Phe) > L (Leu) Missense Variant
PTEN transcript variant 1 NM_000314.8:c.723T>C F [TTT] > F [TTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN NP_000305.3:p.Phe241= F (Phe) > F (Phe) Synonymous Variant
PTEN transcript variant 1 NM_000314.8:c.723T>G F [TTT] > L [TTG] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN NP_000305.3:p.Phe241Leu F (Phe) > L (Leu) Missense 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: C (allele ID: 212819 )
ClinVar Accession Disease Names Clinical Significance
RCV000200168.2 not provided Likely-Benign
RCV000223179.2 Hereditary cancer-predisposing syndrome Likely-Benign
Allele: G (allele ID: 419744 )
ClinVar Accession Disease Names Clinical Significance
RCV000491710.1 Hereditary cancer-predisposing 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 11834 T=1.00000 C=0.00000
European Sub 6970 T=1.0000 C=0.0000
African Sub 3408 T=1.0000 C=0.0000
African Others Sub 114 T=1.000 C=0.000
African American Sub 3294 T=1.0000 C=0.0000
Asian Sub 108 T=1.000 C=0.000
East Asian Sub 84 T=1.00 C=0.00
Other Asian Sub 24 T=1.00 C=0.00
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=1.000 C=0.000
South Asian Sub 94 T=1.00 C=0.00
Other Sub 498 T=1.000 C=0.000


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 251452 T=0.999992 C=0.000008
gnomAD - Exomes European Sub 135394 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 49004 T=0.99996 C=0.00004
gnomAD - Exomes American Sub 34578 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16256 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6140 T=1.0000 C=0.0000
ExAC Global Study-wide 121376 T=0.999992 C=0.000008
ExAC Europe Sub 73342 T=1.00000 C=0.00000
ExAC Asian Sub 25162 T=0.99996 C=0.00004
ExAC American Sub 11558 T=1.00000 C=0.00000
ExAC African Sub 10406 T=1.00000 C=0.00000
ExAC Other Sub 908 T=1.000 C=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 T=1.0000 C=0.0000
ALFA Total Global 1154 T=1.0000 C=0.0000
ALFA African Sub 1114 T=1.0000 C=0.0000
ALFA Other Sub 32 T=1.00 C=0.00
ALFA European Sub 8 T=1.0 C=0.0
ALFA Latin American 1 Sub 0 T=0 C=0
ALFA Latin American 2 Sub 0 T=0 C=0
ALFA South Asian Sub 0 T=0 C=0
ALFA Asian Sub 0 T=0 C=0
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= C G
GRCh38.p12 chr 10 NC_000010.11:g.87957941= NC_000010.11:g.87957941T>C NC_000010.11:g.87957941T>G
GRCh37.p13 chr 10 NC_000010.10:g.89717698= NC_000010.10:g.89717698T>C NC_000010.10:g.89717698T>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.99503= NG_007466.2:g.99503T>C NG_007466.2:g.99503T>G
PTEN transcript variant 1 NM_000314.8:c.723= NM_000314.8:c.723T>C NM_000314.8:c.723T>G
PTEN transcript variant 1 NM_000314.7:c.723= NM_000314.7:c.723T>C NM_000314.7:c.723T>G
PTEN transcript variant 1 NM_000314.6:c.723= NM_000314.6:c.723T>C NM_000314.6:c.723T>G
PTEN transcript NM_000314.4:c.723= NM_000314.4:c.723T>C NM_000314.4:c.723T>G
PTEN transcript variant 1 NM_001304717.5:c.1242= NM_001304717.5:c.1242T>C NM_001304717.5:c.1242T>G
PTEN transcript variant 1 NM_001304717.4:c.1242= NM_001304717.4:c.1242T>C NM_001304717.4:c.1242T>G
PTEN transcript variant 1 NM_001304717.3:c.1242= NM_001304717.3:c.1242T>C NM_001304717.3:c.1242T>G
PTEN transcript variant 1 NM_001304717.2:c.1242= NM_001304717.2:c.1242T>C NM_001304717.2:c.1242T>G
PTEN transcript variant 2 NM_001304718.2:c.132= NM_001304718.2:c.132T>C NM_001304718.2:c.132T>G
PTEN transcript variant 2 NM_001304718.1:c.132= NM_001304718.1:c.132T>C NM_001304718.1:c.132T>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.173730= NW_013171807.1:g.173730T>C NW_013171807.1:g.173730T>G
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN NP_000305.3:p.Phe241= NP_000305.3:p.Phe241= NP_000305.3:p.Phe241Leu
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.4:p.Phe414= NP_001291646.4:p.Phe414= NP_001291646.4:p.Phe414Leu
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform 3 NP_001291647.1:p.Phe44= NP_001291647.1:p.Phe44= NP_001291647.1:p.Phe44Leu
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN isoform PTEN-L NP_001291646.2:p.Phe414= NP_001291646.2:p.Phe414= NP_001291646.2:p.Phe414Leu
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#.

12 SubSNP, 4 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 IMCJ-GDT ss28503392 Sep 24, 2004 (123)
2 ILLUMINA ss75001804 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119896401 Dec 01, 2009 (131)
4 ILLUMINA ss172911469 Jul 04, 2010 (132)
5 ILLUMINA ss536989071 Sep 08, 2015 (146)
6 EVA_EXAC ss1689987344 Apr 01, 2015 (144)
7 CLINVAR ss2137536594 Jun 27, 2017 (150)
8 GNOMAD ss2738382686 Nov 08, 2017 (151)
9 ILLUMINA ss3626499439 Oct 12, 2018 (152)
10 ILLUMINA ss3637864269 Oct 12, 2018 (152)
11 ILLUMINA ss3642866523 Oct 12, 2018 (152)
12 KRGDB ss3922849545 Apr 26, 2020 (154)
13 ExAC NC_000010.10 - 89717698 Oct 12, 2018 (152)
14 gnomAD - Exomes NC_000010.10 - 89717698 Jul 13, 2019 (153)
15 KOREAN population from KRGDB NC_000010.10 - 89717698 Apr 26, 2020 (154)
16 dbGaP Population Frequency Project NC_000010.11 - 87957941 Apr 26, 2020 (154)
17 ClinVar RCV000200168.2 Apr 26, 2020 (154)
18 ClinVar RCV000223179.2 Oct 12, 2018 (152)
19 ClinVar RCV000491710.1 Oct 12, 2018 (152)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3642866523 NC_000010.9:89707677:T:C NC_000010.11:87957940:T:C (self)
214760, 7581603, 30026939, ss536989071, ss1689987344, ss2738382686, ss3626499439, ss3637864269, ss3922849545 NC_000010.10:89717697:T:C NC_000010.11:87957940:T:C (self)
RCV000200168.2, RCV000223179.2, 164382297 NC_000010.11:87957940:T:C NC_000010.11:87957940:T:C (self)
ss28503392, ss75001804, ss119896401, ss172911469 NT_030059.13:40522161:T:C NC_000010.11:87957940:T:C (self)
RCV000491710.1, ss2137536594 NC_000010.11:87957940:T:G NC_000010.11:87957940: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.

No publications for rs17849090

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