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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.

rs1044322

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:87863566 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.012097 (1519/125568, TOPMED)
A=0.0110 (55/5008, 1000G)
A=0.0084 (41/4868, ALFA Project) (+ 12 more)
A=0.0167 (75/4480, Estonian)
A=0.0011 (3/2852, KOREAN)
A=0.0017 (3/1772, Korea1K)
A=0.0196 (22/1124, Daghestan)
A=0.020 (12/600, NorthernSweden)
A=0.037 (8/216, Qatari)
A=0.005 (1/216, Vietnamese)
A=0.03 (1/40, GENOME_DK)
G=0.50 (7/14, SGDP_PRJ)
A=0.50 (7/14, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
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.87863566G>A
GRCh38.p12 chr 10 NC_000010.11:g.87863566G>C
GRCh38.p12 chr 10 NC_000010.11:g.87863566G>T
GRCh37.p13 chr 10 NC_000010.10:g.89623323G>A
GRCh37.p13 chr 10 NC_000010.10:g.89623323G>C
GRCh37.p13 chr 10 NC_000010.10:g.89623323G>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5129G>A
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5129G>C
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5129G>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79390G>A
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79390G>C
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79390G>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4872C>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4872C>G
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4872C>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: 142540 )
ClinVar Accession Disease Names Clinical Significance
RCV000127650.3 not specified Benign
RCV000710303.1 PTEN hamartoma tumor syndrome Benign
RCV000760054.1 not provided Benign
Allele: C (allele ID: 407965 )
ClinVar Accession Disease Names Clinical Significance
RCV000485599.1 not specified Uncertain-Significance
Allele: T (allele ID: 810067 )
ClinVar Accession Disease Names Clinical Significance
RCV001018697.1 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 25830 G=0.99168 A=0.00832, C=0.00000, T=0.00000
European Sub 18574 G=0.98961 A=0.01039, C=0.00000, T=0.00000
African Sub 5554 G=0.9968 A=0.0032, C=0.0000, T=0.0000
African Others Sub 198 G=1.000 A=0.000, C=0.000, T=0.000
African American Sub 5356 G=0.9966 A=0.0034, C=0.0000, T=0.0000
Asian Sub 112 G=1.000 A=0.000, C=0.000, T=0.000
East Asian Sub 86 G=1.00 A=0.00, C=0.00, T=0.00
Other Asian Sub 26 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 1 Sub 132 G=1.000 A=0.000, C=0.000, T=0.000
Latin American 2 Sub 604 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 94 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 760 G=0.995 A=0.005, C=0.000, 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 G=0.987903 A=0.012097
1000Genomes Global Study-wide 5008 G=0.9890 A=0.0110
1000Genomes African Sub 1322 G=0.9909 A=0.0091
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9771 A=0.0229
1000Genomes South Asian Sub 978 G=0.991 A=0.009
1000Genomes American Sub 694 G=0.984 A=0.016
ALFA Total Global 4868 G=0.9916 A=0.0084
ALFA African Sub 2710 G=0.9952 A=0.0048
ALFA European Sub 2072 G=0.9870 A=0.0130
ALFA Other Sub 78 G=0.99 A=0.01
ALFA South Asian Sub 4 G=1.0 A=0.0
ALFA Asian Sub 4 G=1.0 A=0.0
ALFA Latin American 1 Sub 0 G=0 A=0
ALFA Latin American 2 Sub 0 G=0 A=0
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9833 A=0.0167
KOREAN population from KRGDB KOREAN Study-wide 2852 G=0.9989 A=0.0011
Korean Genome Project KOREAN Study-wide 1772 G=0.9983 A=0.0017
Genome-wide autozygosity in Daghestan Global Study-wide 1124 G=0.9804 A=0.0196
Genome-wide autozygosity in Daghestan Daghestan Sub 622 G=0.979 A=0.021
Genome-wide autozygosity in Daghestan Near_East Sub 142 G=0.986 A=0.014
Genome-wide autozygosity in Daghestan Central Asia Sub 120 G=0.983 A=0.017
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.981 A=0.019
Genome-wide autozygosity in Daghestan South Asian Sub 96 G=0.99 A=0.01
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.94 A=0.06
Northern Sweden ACPOP Study-wide 600 G=0.980 A=0.020
Qatari Global Study-wide 216 G=0.963 A=0.037
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.995 A=0.005
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
SGDP_PRJ Global Study-wide 14 G=0.50 A=0.50
Siberian Global Study-wide 2 G=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 G= A C T
GRCh38.p12 chr 10 NC_000010.11:g.87863566= NC_000010.11:g.87863566G>A NC_000010.11:g.87863566G>C NC_000010.11:g.87863566G>T
GRCh37.p13 chr 10 NC_000010.10:g.89623323= NC_000010.10:g.89623323G>A NC_000010.10:g.89623323G>C NC_000010.10:g.89623323G>T
PTEN RefSeqGene (LRG_311) NG_007466.2:g.5129= NG_007466.2:g.5129G>A NG_007466.2:g.5129G>C NG_007466.2:g.5129G>T
PTEN transcript NM_000314.4:c.-903= NM_000314.4:c.-903G>A NM_000314.4:c.-903G>C NM_000314.4:c.-903G>T
chr 10 fix patch HG2334_PATCH NW_013171807.1:g.79390= NW_013171807.1:g.79390G>A NW_013171807.1:g.79390G>C NW_013171807.1:g.79390G>T
KLLN RefSeqGene (LRG_1087) NG_033079.1:g.4872= NG_033079.1:g.4872C>T NG_033079.1:g.4872C>G NG_033079.1:g.4872C>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#.

32 SubSNP, 15 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 LEE ss1513370 Oct 05, 2000 (86)
2 EGP_SNPS ss38349667 Mar 15, 2006 (126)
3 SI_EXO ss61710852 Oct 16, 2006 (127)
4 1000GENOMES ss461790591 Sep 17, 2011 (135)
5 ILLUMINA ss482681019 May 04, 2012 (137)
6 ILLUMINA ss483757162 May 04, 2012 (137)
7 SSMP ss657122673 Apr 25, 2013 (138)
8 ILLUMINA ss782322170 Sep 08, 2015 (146)
9 EVA-GONL ss987753819 Aug 21, 2014 (142)
10 1000GENOMES ss1338437040 Aug 21, 2014 (142)
11 HAMMER_LAB ss1397587996 Sep 08, 2015 (146)
12 DDI ss1426397428 Apr 01, 2015 (144)
13 CLINVAR ss1537038146 Jan 16, 2015 (142)
14 EVA_GENOME_DK ss1575269144 Apr 01, 2015 (144)
15 EVA_DECODE ss1597426762 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1931122223 Feb 12, 2016 (147)
17 JJLAB ss2026288824 Sep 14, 2016 (149)
18 CLINVAR ss2137523309 Jun 02, 2017 (150)
19 USC_VALOUEV ss2154564351 Dec 20, 2016 (150)
20 HUMAN_LONGEVITY ss2176762810 Dec 20, 2016 (150)
21 TOPMED ss2339866149 Dec 20, 2016 (150)
22 SWEGEN ss3006888876 Nov 08, 2017 (151)
23 TOPMED ss3126304065 Nov 08, 2017 (151)
24 ILLUMINA ss3651618434 Oct 12, 2018 (152)
25 EGCUT_WGS ss3674298528 Jul 13, 2019 (153)
26 EVA_DECODE ss3690368797 Jul 13, 2019 (153)
27 ACPOP ss3737543553 Jul 13, 2019 (153)
28 EVA ss3748411479 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3813778960 Jul 13, 2019 (153)
30 SGDP_PRJ ss3874732487 Apr 26, 2020 (154)
31 KRGDB ss3922848168 Apr 26, 2020 (154)
32 KOGIC ss3968369651 Apr 26, 2020 (154)
33 1000Genomes NC_000010.10 - 89623323 Oct 12, 2018 (152)
34 Genome-wide autozygosity in Daghestan NC_000010.9 - 89613303 Apr 26, 2020 (154)
35 Genetic variation in the Estonian population NC_000010.10 - 89623323 Oct 12, 2018 (152)
36 The Danish reference pan genome NC_000010.10 - 89623323 Apr 26, 2020 (154)
37 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138954981 (NC_000010.10:89623322:G:G 30888/31238, NC_000010.10:89623322:G:A 350/31238)
Row 138954982 (NC_000010.10:89623322:G:G 31237/31238, NC_000010.10:89623322:G:C 1/31238)

- Jul 13, 2019 (153)
38 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 138954981 (NC_000010.10:89623322:G:G 30888/31238, NC_000010.10:89623322:G:A 350/31238)
Row 138954982 (NC_000010.10:89623322:G:G 31237/31238, NC_000010.10:89623322:G:C 1/31238)

- Jul 13, 2019 (153)
39 KOREAN population from KRGDB NC_000010.10 - 89623323 Apr 26, 2020 (154)
40 Korean Genome Project NC_000010.11 - 87863566 Apr 26, 2020 (154)
41 Northern Sweden NC_000010.10 - 89623323 Jul 13, 2019 (153)
42 Qatari NC_000010.10 - 89623323 Apr 26, 2020 (154)
43 SGDP_PRJ NC_000010.10 - 89623323 Apr 26, 2020 (154)
44 Siberian NC_000010.10 - 89623323 Apr 26, 2020 (154)
45 TopMed NC_000010.11 - 87863566 Oct 12, 2018 (152)
46 A Vietnamese Genetic Variation Database NC_000010.10 - 89623323 Jul 13, 2019 (153)
47 dbGaP Population Frequency Project NC_000010.11 - 87863566 Apr 26, 2020 (154)
48 ClinVar RCV000127650.3 Apr 26, 2020 (154)
49 ClinVar RCV000485599.1 Oct 12, 2018 (152)
50 ClinVar RCV000710303.1 Jul 13, 2019 (153)
51 ClinVar RCV000760054.1 Jul 13, 2019 (153)
52 ClinVar RCV001018697.1 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
59441, ss482681019, ss1397587996, ss1597426762 NC_000010.9:89613302:G:A NC_000010.11:87863565:G:A (self)
50861339, 20036776, 2263808, 30025562, 10828418, 13164153, 26749467, 7080705, 6269820, ss461790591, ss483757162, ss657122673, ss782322170, ss987753819, ss1338437040, ss1426397428, ss1575269144, ss1931122223, ss2026288824, ss2154564351, ss2339866149, ss3006888876, ss3651618434, ss3674298528, ss3737543553, ss3748411479, ss3874732487, ss3922848168 NC_000010.10:89623322:G:A NC_000010.11:87863565:G:A (self)
RCV000127650.3, RCV000710303.1, RCV000760054.1, 24747652, 48115334, 818313096, ss1537038146, ss2176762810, ss3126304065, ss3690368797, ss3813778960, ss3968369651 NC_000010.11:87863565:G:A NC_000010.11:87863565:G:A (self)
ss61710852 NT_030059.12:8371838:G:A NC_000010.11:87863565:G:A (self)
ss1513370, ss38349667 NT_030059.13:40427786:G:A NC_000010.11:87863565:G:A (self)
NC_000010.10:89623322:G:C NC_000010.11:87863565:G:C (self)
RCV000485599.1, ss2137523309 NC_000010.11:87863565:G:C NC_000010.11:87863565:G:C (self)
RCV001018697.1 NC_000010.11:87863565:G:T NC_000010.11:87863565:G:T
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 rs1044322
PMID Title Author Year Journal
21633361 Germ-line sequence variants of PTEN do not have an important role in hereditary and non-hereditary prostate cancer susceptibility. Xie CC et al. 2011 Journal of human genetics
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