Name: rs2492395
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.

rs2492395

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:19454220 (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: C>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.026778 (7088/264690, TOPMED)
C=0.025051 (3513/140236, GnomAD)
C=0.00000 (0/28258, 14KJPN) (+ 13 more)
C=0.01276 (241/18890, ALFA)
C=0.00000 (0/16760, 8.3KJPN)
C=0.0292 (187/6404, 1000G_30x)
C=0.0280 (140/5008, 1000G)
C=0.0000 (0/3854, ALSPAC)
C=0.0003 (1/3708, TWINSUK)
C=0.0003 (1/2930, KOREAN)
C=0.0000 (0/1832, Korea1K)
C=0.000 (0/600, NorthernSweden)
C=0.009 (5/558, SGDP_PRJ)
C=0.003 (1/322, HapMap)
C=0.023 (5/216, Qatari)
C=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TPTE2 : Intron Variant
Publications: 0 citations
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	C=0.01276	T=0.98724
European	Sub	14286	C=0.00007	T=0.99993
African	Sub	2946	C=0.0737	T=0.9263
African Others	Sub	114	C=0.088	T=0.912
African American	Sub	2832	C=0.0731	T=0.9269
Asian	Sub	112	C=0.000	T=1.000
East Asian	Sub	86	C=0.00	T=1.00
Other Asian	Sub	26	C=0.00	T=1.00
Latin American 1	Sub	146	C=0.000	T=1.000
Latin American 2	Sub	610	C=0.007	T=0.993
South Asian	Sub	98	C=0.00	T=1.00
Other	Sub	692	C=0.027	T=0.973

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.026778	T=0.973222
gnomAD - Genomes	Global	Study-wide	140236	C=0.025051	T=0.974949
gnomAD - Genomes	European	Sub	75974	C=0.00016	T=0.99984
gnomAD - Genomes	African	Sub	42004	C=0.07980	T=0.92020
gnomAD - Genomes	American	Sub	13648	C=0.00769	T=0.99231
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.0000	T=1.0000
gnomAD - Genomes	East Asian	Sub	3134	C=0.0000	T=1.0000
gnomAD - Genomes	Other	Sub	2152	C=0.0204	T=0.9796
14KJPN	JAPANESE	Study-wide	28258	C=0.00000	T=1.00000
Allele Frequency Aggregator	Total	Global	18890	C=0.01276	T=0.98724
Allele Frequency Aggregator	European	Sub	14286	C=0.00007	T=0.99993
Allele Frequency Aggregator	African	Sub	2946	C=0.0737	T=0.9263
Allele Frequency Aggregator	Other	Sub	692	C=0.027	T=0.973
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.007	T=0.993
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.000	T=1.000
Allele Frequency Aggregator	Asian	Sub	112	C=0.000	T=1.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.00	T=1.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.00000	T=1.00000
1000Genomes_30x	Global	Study-wide	6404	C=0.0292	T=0.9708
1000Genomes_30x	African	Sub	1786	C=0.0969	T=0.9031
1000Genomes_30x	Europe	Sub	1266	C=0.0000	T=1.0000
1000Genomes_30x	South Asian	Sub	1202	C=0.0000	T=1.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.0000	T=1.0000
1000Genomes_30x	American	Sub	980	C=0.014	T=0.986
1000Genomes	Global	Study-wide	5008	C=0.0280	T=0.9720
1000Genomes	African	Sub	1322	C=0.0983	T=0.9017
1000Genomes	East Asian	Sub	1008	C=0.0000	T=1.0000
1000Genomes	Europe	Sub	1006	C=0.0000	T=1.0000
1000Genomes	South Asian	Sub	978	C=0.000	T=1.000
1000Genomes	American	Sub	694	C=0.014	T=0.986
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0000	T=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0003	T=0.9997
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0003	A=0.0000, G=0.0000, T=0.9997
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0000	T=1.0000
Northern Sweden	ACPOP	Study-wide	600	C=0.000	T=1.000
SGDP_PRJ	Global	Study-wide	558	C=0.009	T=0.991
HapMap	Global	Study-wide	322	C=0.003	T=0.997
HapMap	American	Sub	120	C=0.000	T=1.000
HapMap	African	Sub	116	C=0.009	T=0.991
HapMap	Asian	Sub	86	C=0.00	T=1.00
Qatari	Global	Study-wide	216	C=0.023	T=0.977
The Danish reference pan genome	Danish	Study-wide	40	C=0.00	T=1.00

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 13	NC_000013.11:g.19454220C>A
GRCh38.p14 chr 13	NC_000013.11:g.19454220C>G
GRCh38.p14 chr 13	NC_000013.11:g.19454220C>T
GRCh37.p13 chr 13	NC_000013.10:g.20028360C>A
GRCh37.p13 chr 13	NC_000013.10:g.20028360C>G
GRCh37.p13 chr 13	NC_000013.10:g.20028360C>T

Gene: TPTE2, transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TPTE2 transcript variant 4	NM_001141968.2:c.409-2995… NM_001141968.2:c.409-2995G>T	N/A	Intron Variant
TPTE2 transcript variant 9	NM_001395978.1:c.742-2995… NM_001395978.1:c.742-2995G>T	N/A	Intron Variant
TPTE2 transcript variant 1	NM_130785.4:c.511-2995G>T	N/A	Intron Variant
TPTE2 transcript variant 3	NM_199254.3:c.742-2995G>T	N/A	Intron Variant
TPTE2 transcript variant 5	NM_001271850.2:c.	N/A	Genic Upstream Transcript Variant
TPTE2 transcript variant 6	NR_073485.2:n.	N/A	Intron Variant
TPTE2 transcript variant 7	NR_073486.1:n.	N/A	Intron Variant
TPTE2 transcript variant 8	NR_073487.2:n.	N/A	Intron 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.

Not Reported in ClinVar

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.p14 chr 13	NC_000013.11:g.19454220=	NC_000013.11:g.19454220C>A	NC_000013.11:g.19454220C>G	NC_000013.11:g.19454220C>T
GRCh37.p13 chr 13	NC_000013.10:g.20028360=	NC_000013.10:g.20028360C>A	NC_000013.10:g.20028360C>G	NC_000013.10:g.20028360C>T
TPTE2 transcript variant 4	NM_001141968.1:c.409-2995=	NM_001141968.1:c.409-2995G>T	NM_001141968.1:c.409-2995G>C	NM_001141968.1:c.409-2995G>A
TPTE2 transcript variant 4	NM_001141968.2:c.409-2995=	NM_001141968.2:c.409-2995G>T	NM_001141968.2:c.409-2995G>C	NM_001141968.2:c.409-2995G>A
TPTE2 transcript variant 9	NM_001395978.1:c.742-2995=	NM_001395978.1:c.742-2995G>T	NM_001395978.1:c.742-2995G>C	NM_001395978.1:c.742-2995G>A
TPTE2 transcript variant 1	NM_130785.3:c.511-2995=	NM_130785.3:c.511-2995G>T	NM_130785.3:c.511-2995G>C	NM_130785.3:c.511-2995G>A
TPTE2 transcript variant 1	NM_130785.4:c.511-2995=	NM_130785.4:c.511-2995G>T	NM_130785.4:c.511-2995G>C	NM_130785.4:c.511-2995G>A
TPTE2 transcript variant 3	NM_199254.2:c.742-2995=	NM_199254.2:c.742-2995G>T	NM_199254.2:c.742-2995G>C	NM_199254.2:c.742-2995G>A
TPTE2 transcript variant 3	NM_199254.3:c.742-2995=	NM_199254.3:c.742-2995G>T	NM_199254.3:c.742-2995G>C	NM_199254.3:c.742-2995G>A

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#.

67 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3497131	Sep 28, 2001 (100)
2	SC_JCM	ss4222637	Nov 05, 2001 (101)
3	BCM_SSAHASNP	ss11081931	Jul 11, 2003 (116)
4	WI_SSAHASNP	ss12252054	Jul 11, 2003 (116)
5	SC_SNP	ss13157389	Dec 05, 2003 (119)
6	CSHL-HAPMAP	ss16619038	Feb 27, 2004 (120)
7	SSAHASNP	ss21074855	Apr 05, 2004 (121)
8	ABI	ss40299217	Mar 13, 2006 (126)
9	HGSV	ss81259036	Dec 15, 2007 (130)
10	HGSV	ss84649043	Dec 15, 2007 (130)
11	BCMHGSC_JDW	ss89505303	Mar 24, 2008 (129)
12	HUMANGENOME_JCVI	ss96947464	Feb 04, 2009 (130)
13	ENSEMBL	ss133459676	Dec 01, 2009 (131)
14	ENSEMBL	ss137299472	Dec 01, 2009 (131)
15	GMI	ss158107262	Dec 01, 2009 (131)
16	BCM-HGSC-SUB	ss206793013	Jul 04, 2010 (132)
17	BL	ss254813468	May 09, 2011 (134)
18	GMI	ss281621183	May 04, 2012 (137)
19	GMI	ss286659708	Apr 25, 2013 (138)
20	PJP	ss291547299	May 09, 2011 (134)
21	1000GENOMES	ss337735664	May 09, 2011 (134)
22	TISHKOFF	ss563523452	Apr 25, 2013 (138)
23	SSMP	ss659115197	Apr 25, 2013 (138)
24	JMKIDD_LAB	ss1078905267	Aug 21, 2014 (142)
25	1000GENOMES	ss1347342616	Aug 21, 2014 (142)
26	DDI	ss1427112891	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1576639070	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1629808897	Apr 01, 2015 (144)
29	EVA_DECODE	ss1642255244	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1672802930	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1807505939	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1933514664	Feb 12, 2016 (147)
33	GENOMED	ss1967723081	Jul 19, 2016 (147)
34	JJLAB	ss2027510721	Sep 14, 2016 (149)
35	SYSTEMSBIOZJU	ss2628241979	Nov 08, 2017 (151)
36	GRF	ss2700243511	Nov 08, 2017 (151)
37	GNOMAD	ss2917171259	Nov 08, 2017 (151)
38	SWEGEN	ss3010652323	Nov 08, 2017 (151)
39	CSHL	ss3350342609	Nov 08, 2017 (151)
40	URBANLAB	ss3649975967	Oct 12, 2018 (152)
41	EVA_DECODE	ss3694843725	Jul 13, 2019 (153)
42	ACPOP	ss3739544251	Jul 13, 2019 (153)
43	EVA	ss3751187481	Jul 13, 2019 (153)
44	PACBIO	ss3787390595	Jul 13, 2019 (153)
45	PACBIO	ss3792465917	Jul 13, 2019 (153)
46	PACBIO	ss3797349566	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3816515947	Jul 13, 2019 (153)
48	EVA	ss3833424550	Apr 27, 2020 (154)
49	EVA	ss3840286719	Apr 27, 2020 (154)
50	EVA	ss3845770815	Apr 27, 2020 (154)
51	SGDP_PRJ	ss3879508595	Apr 27, 2020 (154)
52	KRGDB	ss3928317344	Apr 27, 2020 (154)
53	KOGIC	ss3973127787	Apr 27, 2020 (154)
54	TOPMED	ss4938675954	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5209002632	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5292956645	Oct 16, 2022 (156)
57	EVA	ss5409370719	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5487401265	Oct 16, 2022 (156)
59	EVA	ss5510894164	Oct 16, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5591530204	Oct 16, 2022 (156)
61	SANFORD_IMAGENETICS	ss5654319223	Oct 16, 2022 (156)
62	TOMMO_GENOMICS	ss5760592335	Oct 16, 2022 (156)
63	YY_MCH	ss5813911950	Oct 16, 2022 (156)
64	EVA	ss5839163825	Oct 16, 2022 (156)
65	EVA	ss5850628337	Oct 16, 2022 (156)
66	EVA	ss5924218016	Oct 16, 2022 (156)
67	EVA	ss5945725808	Oct 16, 2022 (156)
68	1000Genomes	NC_000013.10 - 20028360	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000013.11 - 19454220	Oct 16, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 20028360	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000013.10 - 20028360	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000013.11 - 19454220	Apr 26, 2021 (155)
73	HapMap	NC_000013.11 - 19454220	Apr 27, 2020 (154)
74	KOREAN population from KRGDB	NC_000013.10 - 20028360	Apr 27, 2020 (154)
75	Korean Genome Project	NC_000013.11 - 19454220	Apr 27, 2020 (154)
76	Northern Sweden	NC_000013.10 - 20028360	Jul 13, 2019 (153)
77	Qatari	NC_000013.10 - 20028360	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000013.10 - 20028360	Apr 27, 2020 (154)
79	8.3KJPN	NC_000013.10 - 20028360	Apr 26, 2021 (155)
80	14KJPN	NC_000013.11 - 19454220	Oct 16, 2022 (156)
81	TopMed	NC_000013.11 - 19454220	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000013.10 - 20028360	Oct 12, 2018 (152)
83	ALFA	NC_000013.11 - 19454220	Apr 26, 2021 (155)

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).

Associated ID	History Updated (Build)
rs58343729	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35494738, ss3928317344	NC_000013.10:20028359:C:A	NC_000013.11:19454219:C:A	(self)
35494738, ss3928317344	NC_000013.10:20028359:C:G	NC_000013.11:19454219:C:G	(self)
ss81259036, ss84649043, ss89505303, ss206793013, ss254813468, ss281621183, ss286659708, ss291547299, ss1642255244	NC_000013.9:18926359:C:T	NC_000013.11:19454219:C:T	(self)
60179538, 33418849, 3201134, 35494738, 12829116, 15556594, 31525575, 66971939, 33418849, ss337735664, ss563523452, ss659115197, ss1078905267, ss1347342616, ss1427112891, ss1576639070, ss1629808897, ss1672802930, ss1807505939, ss1933514664, ss1967723081, ss2027510721, ss2628241979, ss2700243511, ss2917171259, ss3010652323, ss3350342609, ss3739544251, ss3751187481, ss3787390595, ss3792465917, ss3797349566, ss3833424550, ss3840286719, ss3879508595, ss3928317344, ss5209002632, ss5409370719, ss5510894164, ss5654319223, ss5839163825, ss5945725808	NC_000013.10:20028359:C:T	NC_000013.11:19454219:C:T	(self)
79056139, 424436900, 939564, 29505788, 94429439, 154221612, 13659952622, ss3649975967, ss3694843725, ss3816515947, ss3845770815, ss3973127787, ss4938675954, ss5292956645, ss5487401265, ss5591530204, ss5760592335, ss5813911950, ss5850628337, ss5924218016	NC_000013.11:19454219:C:T	NC_000013.11:19454219:C:T	(self)
ss11081931, ss12252054, ss13157389	NT_009799.12:1008359:C:T	NC_000013.11:19454219:C:T	(self)
ss16619038, ss21074855	NT_024524.13:1008359:C:T	NC_000013.11:19454219:C:T	(self)
ss3497131, ss4222637, ss40299217, ss96947464, ss133459676, ss137299472, ss158107262	NT_024524.14:1008359:C:T	NC_000013.11:19454219:C:T	(self)

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

No publications for rs2492395

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2492395