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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.

rs34248932

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87875205 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.003034 (381/125568, TOPMED)
C=0.00233 (73/31326, GnomAD)
C=0.0048 (24/5008, 1000G) (+ 6 more)
C=0.0016 (6/3854, ALSPAC)
C=0.0022 (8/3708, TWINSUK)
C=0.0014 (3/2188, ALFA Project)
C=0.001 (1/998, GoNL)
C=0.002 (1/600, NorthernSweden)
C=0.009 (2/216, Qatari)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : Intron Variant
LOC107987150 : Non Coding Transcript 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.87875205T>C
GRCh37.p13 chr 10 NC_000010.10:g.89634962T>C
PTEN RefSeqGene (LRG_311) NG_007466.2:g.16767T>C
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.91029T>C
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+10657T>C N/A Intron Variant
PTEN transcript variant 1 NM_001304717.5:c.599+1065…

NM_001304717.5:c.599+10657T>C

N/A Intron Variant
PTEN transcript variant 2 NM_001304718.2:c.-627+106…

NM_001304718.2:c.-627+10657T>C

N/A Intron Variant
Gene: LOC107987150, uncharacterized LOC107987150 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107987150 transcript XR_001747529.1:n.1983T>C N/A Non Coding Transcript 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: 225675 )
ClinVar Accession Disease Names Clinical Significance
RCV000208970.1 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 14420 T=0.99771 C=0.00229
European Sub 9824 T=0.9990 C=0.0010
African Sub 2946 T=0.9939 C=0.0061
African Others Sub 114 T=0.982 C=0.018
African American Sub 2832 T=0.9944 C=0.0056
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=0.993 C=0.007
South Asian Sub 98 T=1.00 C=0.00
Other Sub 684 T=0.999 C=0.001


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
TopMed Global Study-wide 125568 T=0.996966 C=0.003034
gnomAD - Genomes Global Study-wide 31326 T=0.99767 C=0.00233
gnomAD - Genomes European Sub 18834 T=0.99904 C=0.00096
gnomAD - Genomes African Sub 8712 T=0.9948 C=0.0052
gnomAD - Genomes East Asian Sub 1560 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 1086 T=0.9963 C=0.0037
gnomAD - Genomes American Sub 846 T=0.993 C=0.007
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=1.000 C=0.000
1000Genomes Global Study-wide 5008 T=0.9952 C=0.0048
1000Genomes African Sub 1322 T=0.9887 C=0.0113
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9950 C=0.0050
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.994 C=0.006
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9984 C=0.0016
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9978 C=0.0022
ALFA Total Global 2188 T=0.9986 C=0.0014
ALFA European Sub 2072 T=0.9990 C=0.0010
ALFA African Sub 82 T=0.99 C=0.01
ALFA Other Sub 26 T=1.00 C=0.00
ALFA South Asian Sub 4 T=1.0 C=0.0
ALFA Asian Sub 4 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
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.999 C=0.001
Northern Sweden ACPOP Study-wide 600 T=0.998 C=0.002
Qatari Global Study-wide 216 T=0.991 C=0.009
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
GRCh38.p12 chr 10 NC_000010.11:g.87875205= NC_000010.11:g.87875205T>C
GRCh37.p13 chr 10 NC_000010.10:g.89634962= NC_000010.10:g.89634962T>C
PTEN RefSeqGene (LRG_311) NG_007466.2:g.16767= NG_007466.2:g.16767T>C
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.91029= NW_013171807.1:g.91029T>C
LOC107987150 transcript XR_001747529.1:n.1983= XR_001747529.1:n.1983T>C
PTEN transcript NM_000314.4:c.79+10657= NM_000314.4:c.79+10657T>C
PTEN transcript variant 1 NM_000314.6:c.79+10658= NM_000314.6:c.79+10658T>C
PTEN transcript variant 1 NM_000314.8:c.79+10657= NM_000314.8:c.79+10657T>C
PTEN transcript variant 1 NM_001304717.2:c.598+10658= NM_001304717.2:c.598+10658T>C
PTEN transcript variant 1 NM_001304717.5:c.599+10657= NM_001304717.5:c.599+10657T>C
PTEN transcript variant 2 NM_001304718.1:c.-627+10658= NM_001304718.1:c.-627+10658T>C
PTEN transcript variant 2 NM_001304718.2:c.-627+10657= NM_001304718.2:c.-627+10657T>C
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#.

17 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss38349690 Mar 13, 2006 (126)
2 1000GENOMES ss235274385 Jul 15, 2010 (132)
3 EVA-GONL ss987753915 Aug 21, 2014 (142)
4 1000GENOMES ss1338437325 Aug 21, 2014 (142)
5 EVA_DECODE ss1597426821 Apr 01, 2015 (144)
6 EVA_UK10K_ALSPAC ss1625093423 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1668087456 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1931122300 Feb 12, 2016 (147)
9 GENOMED ss1967189117 Jul 19, 2016 (147)
10 HUMAN_LONGEVITY ss2176763500 Dec 20, 2016 (150)
11 TOPMED ss2339866872 Dec 20, 2016 (150)
12 GNOMAD ss2891601545 Nov 08, 2017 (151)
13 TOPMED ss3126306383 Nov 08, 2017 (151)
14 EVA_DECODE ss3690368945 Jul 13, 2019 (153)
15 ACPOP ss3737543598 Jul 13, 2019 (153)
16 KHV_HUMAN_GENOMES ss3813779041 Jul 13, 2019 (153)
17 EVA ss3832252649 Apr 26, 2020 (154)
18 1000Genomes NC_000010.10 - 89634962 Oct 12, 2018 (152)
19 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89634962 Oct 12, 2018 (152)
20 gnomAD - Genomes NC_000010.10 - 89634962 Jul 13, 2019 (153)
21 Genome of the Netherlands Release 5 NC_000010.10 - 89634962 Apr 26, 2020 (154)
22 Northern Sweden NC_000010.10 - 89634962 Jul 13, 2019 (153)
23 Qatari NC_000010.10 - 89634962 Apr 26, 2020 (154)
24 TopMed NC_000010.11 - 87875205 Oct 12, 2018 (152)
25 UK 10K study - Twins NC_000010.10 - 89634962 Oct 12, 2018 (152)
26 dbGaP Population Frequency Project NC_000010.11 - 87875205 Apr 26, 2020 (154)
27 ClinVar RCV000208970.1 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
ss1597426821 NC_000010.9:89624941:T:C NC_000010.11:87875204:T:C (self)
50861639, 28232394, 138955936, 12589913, 10828463, 13164230, 28232394, ss235274385, ss987753915, ss1338437325, ss1625093423, ss1668087456, ss1931122300, ss1967189117, ss2339866872, ss2891601545, ss3737543598, ss3832252649 NC_000010.10:89634961:T:C NC_000010.11:87875204:T:C (self)
RCV000208970.1, 48117385, 379964343, ss2176763500, ss3126306383, ss3690368945, ss3813779041 NC_000010.11:87875204:T:C NC_000010.11:87875204:T:C (self)
ss38349690 NT_030059.13:40439425:T:C NC_000010.11:87875204:T:C (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 rs34248932

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