Name: rs1044322
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:87863566 (GRCh38.p14) 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=0.00142 (40/28256, 14KJPN)
A=0.00832 (215/25830, ALFA)
A=0.00173 (29/16758, 8.3KJPN) (+ 13 more)
A=0.0110 (55/5008, 1000G)
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: KLLN : 2KB Upstream Variant
PTEN : 2KB Upstream Variant
Publications: 1 citation
Genomic View: See rs on genome

ALFA Allele Frequency
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	25830	G=0.99168	A=0.00832, C=0.00000, T=0.00000	0.983585	0.000232	0.016183	3
European	Sub	18574	G=0.98961	A=0.01039, C=0.00000, T=0.00000	0.979541	0.000323	0.020136	3
African	Sub	5554	G=0.9968	A=0.0032, C=0.0000, T=0.0000	0.993518	0.0	0.006482	0
African Others	Sub	198	G=1.000	A=0.000, C=0.000, T=0.000	1.0	0.0	0.0	N/A
African American	Sub	5356	G=0.9966	A=0.0034, C=0.0000, T=0.0000	0.993279	0.0	0.006721	0
Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	86	G=1.00	A=0.00, C=0.00, T=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	G=1.00	A=0.00, C=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	132	G=1.000	A=0.000, C=0.000, T=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	604	G=1.000	A=0.000, C=0.000, T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	94	G=1.00	A=0.00, C=0.00, T=0.00	1.0	0.0	0.0	N/A
Other	Sub	760	G=0.995	A=0.005, C=0.000, T=0.000	0.989474	0.0	0.010526	0

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
14KJPN	JAPANESE	Study-wide	28256	G=0.99858	A=0.00142
Allele Frequency Aggregator	Total	Global	25830	G=0.99168	A=0.00832, C=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	18574	G=0.98961	A=0.01039, C=0.00000, T=0.00000
Allele Frequency Aggregator	African	Sub	5554	G=0.9968	A=0.0032, C=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	760	G=0.995	A=0.005, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	604	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	132	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	94	G=1.00	A=0.00, C=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	16758	G=0.99827	A=0.00173
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
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

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.p14 chr 10	NC_000010.11:g.87863566G>A
GRCh38.p14 chr 10	NC_000010.11:g.87863566G>C
GRCh38.p14 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
GRCh38.p14 chr 10 fix patch HG2334_PATCH	NW_013171807.1:g.79390G>A
GRCh38.p14 chr 10 fix patch HG2334_PATCH	NW_013171807.1:g.79390G>C
GRCh38.p14 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 2	NM_001304717.5:c.	N/A	Upstream Transcript Variant
PTEN transcript variant 3	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_001126049.2:c.	N/A	Upstream Transcript 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: A (allele ID: 142540 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000127650.5	not specified	Benign
RCV000710303.3	PTEN hamartoma tumor syndrome	Benign
RCV000760054.6	not provided	Benign

Allele: C (allele ID: 407965 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000485599.2	not specified	Uncertain-Significance
RCV001284222.2	not provided	Uncertain-Significance

Allele: T (allele ID: 810067 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001018697.3	Hereditary cancer-predisposing syndrome	Uncertain-Significance

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.p14 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
GRCh38.p14 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
PTEN transcript variant 1	NM_000314.6:c.-903=	NM_000314.6:c.-903G>A	NM_000314.6:c.-903G>C	NM_000314.6:c.-903G>T
PTEN transcript variant 1	NM_000314.5:c.-903=	NM_000314.5:c.-903G>A	NM_000314.5:c.-903G>C	NM_000314.5:c.-903G>T
PTEN transcript variant 1	NM_001304717.4:c.-384=	NM_001304717.4:c.-384G>A	NM_001304717.4:c.-384G>C	NM_001304717.4:c.-384G>T
PTEN transcript variant 1	NM_001304717.2:c.-384=	NM_001304717.2:c.-384G>A	NM_001304717.2:c.-384G>C	NM_001304717.2:c.-384G>T
PTEN transcript variant 2	NM_001304718.1:c.-1608=	NM_001304718.1:c.-1608G>A	NM_001304718.1:c.-1608G>C	NM_001304718.1:c.-1608G>T
PTEN transcript variant 1	NM_001304717.1:c.-384=	NM_001304717.1:c.-384G>A	NM_001304717.1:c.-384G>C	NM_001304717.1:c.-384G>T

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#.

45 SubSNP, 18 Frequency, 6 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	SWEGEN	ss3006888876	Nov 08, 2017 (151)
22	ILLUMINA	ss3651618434	Oct 12, 2018 (152)
23	EGCUT_WGS	ss3674298528	Jul 13, 2019 (153)
24	EVA_DECODE	ss3690368797	Jul 13, 2019 (153)
25	ACPOP	ss3737543553	Jul 13, 2019 (153)
26	EVA	ss3748411479	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3813778960	Jul 13, 2019 (153)
28	SGDP_PRJ	ss3874732487	Apr 26, 2020 (154)
29	KRGDB	ss3922848168	Apr 26, 2020 (154)
30	KOGIC	ss3968369651	Apr 26, 2020 (154)
31	GNOMAD	ss4222813914	Apr 26, 2021 (155)
32	GNOMAD	ss4222813915	Apr 26, 2021 (155)
33	TOPMED	ss4860996592	Apr 26, 2021 (155)
34	TOPMED	ss4860996593	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5198759940	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5284926870	Oct 16, 2022 (156)
37	EVA	ss5395032217	Oct 16, 2022 (156)
38	HUGCELL_USP	ss5480403012	Oct 16, 2022 (156)
39	EVA	ss5510113053	Oct 16, 2022 (156)
40	SANFORD_IMAGENETICS	ss5649794698	Oct 16, 2022 (156)
41	TOMMO_GENOMICS	ss5744915602	Oct 16, 2022 (156)
42	YY_MCH	ss5811752591	Oct 16, 2022 (156)
43	EVA	ss5824743381	Oct 16, 2022 (156)
44	EVA	ss5879897523	Oct 16, 2022 (156)
45	EVA	ss5941075478	Oct 16, 2022 (156)
46	1000Genomes	NC_000010.10 - 89623323	Oct 12, 2018 (152)
47	Genome-wide autozygosity in Daghestan	NC_000010.9 - 89613303	Apr 26, 2020 (154)
48	Genetic variation in the Estonian population	NC_000010.10 - 89623323	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000010.10 - 89623323	Apr 26, 2020 (154)
50	gnomAD - Genomes Submission ignored due to conflicting rows: Row 359381525 (NC_000010.11:87863565:G:A 1717/140108) Row 359381526 (NC_000010.11:87863565:G:C 2/140114)	-	Apr 26, 2021 (155)
51	gnomAD - Genomes Submission ignored due to conflicting rows: Row 359381525 (NC_000010.11:87863565:G:A 1717/140108) Row 359381526 (NC_000010.11:87863565:G:C 2/140114)	-	Apr 26, 2021 (155)
52	KOREAN population from KRGDB	NC_000010.10 - 89623323	Apr 26, 2020 (154)
53	Korean Genome Project	NC_000010.11 - 87863566	Apr 26, 2020 (154)
54	Northern Sweden	NC_000010.10 - 89623323	Jul 13, 2019 (153)
55	Qatari	NC_000010.10 - 89623323	Apr 26, 2020 (154)
56	SGDP_PRJ	NC_000010.10 - 89623323	Apr 26, 2020 (154)
57	Siberian	NC_000010.10 - 89623323	Apr 26, 2020 (154)
58	8.3KJPN	NC_000010.10 - 89623323	Apr 26, 2021 (155)
59	14KJPN	NC_000010.11 - 87863566	Oct 16, 2022 (156)
60	TopMed Submission ignored due to conflicting rows: Row 76542247 (NC_000010.11:87863565:G:A 3189/264690) Row 76542248 (NC_000010.11:87863565:G:T 1/264690)	-	Apr 26, 2021 (155)
61	TopMed Submission ignored due to conflicting rows: Row 76542247 (NC_000010.11:87863565:G:A 3189/264690) Row 76542248 (NC_000010.11:87863565:G:T 1/264690)	-	Apr 26, 2021 (155)
62	A Vietnamese Genetic Variation Database	NC_000010.10 - 89623323	Jul 13, 2019 (153)
63	ALFA	NC_000010.11 - 87863566	Apr 26, 2021 (155)
64	ClinVar	RCV000127650.5	Oct 16, 2022 (156)
65	ClinVar	RCV000485599.2	Oct 16, 2022 (156)
66	ClinVar	RCV000710303.3	Oct 16, 2022 (156)
67	ClinVar	RCV000760054.6	Oct 16, 2022 (156)
68	ClinVar	RCV001018697.3	Oct 16, 2022 (156)
69	ClinVar	RCV001284222.2	Oct 16, 2022 (156)

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, 56729247, 6269820, ss461790591, ss483757162, ss657122673, ss782322170, ss987753819, ss1338437040, ss1426397428, ss1575269144, ss1931122223, ss2026288824, ss2154564351, ss3006888876, ss3651618434, ss3674298528, ss3737543553, ss3748411479, ss3874732487, ss3922848168, ss5198759940, ss5395032217, ss5510113053, ss5649794698, ss5824743381, ss5941075478	NC_000010.10:89623322:G:A	NC_000010.11:87863565:G:A	(self)
RCV000127650.5, RCV000710303.3, RCV000760054.6, 24747652, 78752706, 4245151480, ss1537038146, ss2176762810, ss3690368797, ss3813778960, ss3968369651, ss4222813914, ss4860996592, ss5284926870, ss5480403012, ss5744915602, ss5811752591, ss5879897523	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)
RCV000485599.2, RCV001284222.2, 4245151480, ss2137523309, ss4222813915	NC_000010.11:87863565:G:C	NC_000010.11:87863565:G:C	(self)
RCV001018697.3, 4245151480, ss4860996593	NC_000010.11:87863565:G:T	NC_000010.11:87863565:G:T	(self)

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

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1044322