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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.

rs34149102

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87863443 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.007056 (886/125568, TOPMED)
A=0.00562 (176/31332, GnomAD)
A=0.0014 (7/5008, 1000G) (+ 8 more)
A=0.0042 (19/4480, Estonian)
A=0.0075 (29/3854, ALSPAC)
A=0.0059 (22/3708, TWINSUK)
A=0.0000 (0/2148, ALFA Project)
T=0.0000 (0/2148, dbGaP Population Frequency Project)
A=0.003 (2/600, NorthernSweden)
C=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTEN : 5 Prime UTR Variant
KLLN : 2KB Upstream Variant
Publications
1 citation
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.87863443C>A
GRCh38.p12 chr 10 NC_000010.11:g.87863443C>G
GRCh38.p12 chr 10 NC_000010.11:g.87863443C>T
GRCh37.p13 chr 10 NC_000010.10:g.89623200C>A
GRCh37.p13 chr 10 NC_000010.10:g.89623200C>G
GRCh37.p13 chr 10 NC_000010.10:g.89623200C>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5006C>A
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5006C>G
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5006C>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79267C>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79267C>G
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79267C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4995G>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4995G>C
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4995G>A
Gene: PTEN, phosphatase and tensin homolog (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
PTEN transcript variant 1 NM_000314.8:c. N/A Upstream Transcript Variant
PTEN transcript variant 1 NM_001304717.5:c. N/A Upstream Transcript Variant
PTEN transcript variant 2 NM_001304718.2:c. N/A Upstream Transcript 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
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: A (allele ID: 142539 )
ClinVar Accession Disease Names Clinical Significance
RCV000127649.3 not specified Benign-Likely-Benign
RCV000710301.2 PTEN hamartoma tumor syndrome Likely-Benign
Allele: G (allele ID: 810053 )
ClinVar Accession Disease Names Clinical Significance
RCV001017016.1 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 18672 C=0.99877 A=0.00123, T=0.00000
European Sub 14094 C=0.99858 A=0.00142, T=0.00000
African Sub 2938 C=1.0000 A=0.0000, T=0.0000
African Others Sub 114 C=1.000 A=0.000, T=0.000
African American Sub 2824 C=1.0000 A=0.0000, T=0.0000
Asian Sub 112 C=1.000 A=0.000, T=0.000
East Asian Sub 86 C=1.00 A=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 600 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 684 C=0.996 A=0.004, T=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
TopMed Global Study-wide 125568 C=0.992936 A=0.007056, T=0.000008
gnomAD - Genomes Global Study-wide 31332 C=0.99438 A=0.00562
gnomAD - Genomes European Sub 18876 C=0.99221 A=0.00779
gnomAD - Genomes African Sub 8680 C=0.9983 A=0.0017
gnomAD - Genomes East Asian Sub 1560 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1086 C=0.9936 A=0.0064
gnomAD - Genomes American Sub 842 C=0.996 A=0.004
gnomAD - Genomes Ashkenazi Jewish Sub 288 C=0.986 A=0.014
1000Genomes Global Study-wide 5008 C=0.9986 A=0.0014
1000Genomes African Sub 1322 C=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=0.9950 A=0.0050
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=0.997 A=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9958 A=0.0042
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9925 A=0.0075
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9941 A=0.0059
ALFA Total Global 2148 C=1.0000 A=0.0000, T=0.0000
ALFA European Sub 2032 C=1.0000 A=0.0000, T=0.0000
ALFA African Sub 82 C=1.00 A=0.00, T=0.00
ALFA Other Sub 26 C=1.00 A=0.00, T=0.00
ALFA South Asian Sub 4 C=1.0 A=0.0, T=0.0
ALFA Asian Sub 4 C=1.0 A=0.0, T=0.0
ALFA Latin American 1 Sub 0 C=0 A=0, T=0
ALFA Latin American 2 Sub 0 C=0 A=0, T=0
Northern Sweden ACPOP Study-wide 600 C=0.997 A=0.003
SGDP_PRJ Global Study-wide 2 C=0.5 A=0.5
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 C= A G T
GRCh38.p12 chr 10 NC_000010.11:g.87863443= NC_000010.11:g.87863443C>A NC_000010.11:g.87863443C>G NC_000010.11:g.87863443C>T
GRCh37.p13 chr 10 NC_000010.10:g.89623200= NC_000010.10:g.89623200C>A NC_000010.10:g.89623200C>G NC_000010.10:g.89623200C>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5006= NG_007466.2:g.5006C>A NG_007466.2:g.5006C>G NG_007466.2:g.5006C>T
PTEN transcript NM_000314.4:c.-1026= NM_000314.4:c.-1026C>A NM_000314.4:c.-1026C>G NM_000314.4:c.-1026C>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79267= NW_013171807.1:g.79267C>A NW_013171807.1:g.79267C>G NW_013171807.1:g.79267C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4995= NG_033079.1:g.4995G>T NG_033079.1:g.4995G>C NG_033079.1:g.4995G>A
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, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss38349666 Mar 13, 2006 (126)
2 1000GENOMES ss1338437036 Aug 21, 2014 (142)
3 EVA_DECODE ss1597426761 Apr 01, 2015 (144)
4 EVA_UK10K_ALSPAC ss1625093238 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1668087271 Apr 01, 2015 (144)
6 JJLAB ss2026288823 Sep 14, 2016 (149)
7 HUMAN_LONGEVITY ss2176762796 Dec 20, 2016 (150)
8 TOPMED ss2339866130 Dec 20, 2016 (150)
9 GNOMAD ss2891600606 Nov 08, 2017 (151)
10 SWEGEN ss3006888874 Nov 08, 2017 (151)
11 TOPMED ss3126304020 Nov 08, 2017 (151)
12 TOPMED ss3126304021 Nov 08, 2017 (151)
13 CSHL ss3349240365 Nov 08, 2017 (151)
14 EGCUT_WGS ss3674298526 Jul 13, 2019 (153)
15 EVA_DECODE ss3690368795 Jul 13, 2019 (153)
16 ACPOP ss3737543551 Jul 13, 2019 (153)
17 SGDP_PRJ ss3874732484 Apr 26, 2020 (154)
18 1000Genomes NC_000010.10 - 89623200 Oct 12, 2018 (152)
19 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 89623200 Oct 12, 2018 (152)
20 Genetic variation in the Estonian population NC_000010.10 - 89623200 Oct 12, 2018 (152)
21 gnomAD - Genomes NC_000010.10 - 89623200 Jul 13, 2019 (153)
22 Northern Sweden NC_000010.10 - 89623200 Jul 13, 2019 (153)
23 SGDP_PRJ NC_000010.10 - 89623200 Apr 26, 2020 (154)
24 TopMed NC_000010.11 - 87863443 Oct 12, 2018 (152)
25 UK 10K study - Twins NC_000010.10 - 89623200 Oct 12, 2018 (152)
26 dbGaP Population Frequency Project NC_000010.11 - 87863443 Apr 26, 2020 (154)
27 ClinVar RCV000127649.3 Oct 12, 2018 (152)
28 ClinVar RCV000710301.2 Apr 26, 2020 (154)
29 ClinVar RCV001017016.1 Apr 26, 2020 (154)
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
ss1597426761 NC_000010.9:89613179:C:A NC_000010.11:87863442:C:A (self)
50861335, 28232190, 20036774, 138954965, 10828416, 26749464, 28232190, ss1338437036, ss1625093238, ss1668087271, ss2026288823, ss2339866130, ss2891600606, ss3006888874, ss3349240365, ss3674298526, ss3737543551, ss3874732484 NC_000010.10:89623199:C:A NC_000010.11:87863442:C:A (self)
RCV000127649.3, RCV000710301.2, 48115299, 632164742, ss2176762796, ss3126304020, ss3690368795 NC_000010.11:87863442:C:A NC_000010.11:87863442:C:A (self)
ss38349666 NT_030059.13:40427663:C:A NC_000010.11:87863442:C:A (self)
RCV001017016.1 NC_000010.11:87863442:C:G NC_000010.11:87863442:C:G
48115299, 632164742, ss3126304021 NC_000010.11:87863442:C:T NC_000010.11:87863442:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs34149102
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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