Name: rs12582043
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.

rs12582043

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:26769140 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.347758 (92048/264690, TOPMED)
A=0.369277 (51684/139960, GnomAD)
A=0.14704 (4155/28258, 14KJPN) (+ 18 more)
A=0.45256 (8548/18888, ALFA)
A=0.14714 (2466/16760, 8.3KJPN)
A=0.2473 (1584/6404, 1000G_30x)
A=0.2456 (1230/5008, 1000G)
G=0.4098 (1835/4478, Estonian)
G=0.4831 (1862/3854, ALSPAC)
G=0.4835 (1793/3708, TWINSUK)
A=0.1805 (529/2930, KOREAN)
G=0.493 (492/998, GoNL)
G=0.465 (279/600, NorthernSweden)
A=0.296 (97/328, HapMap)
A=0.319 (69/216, Qatari)
A=0.196 (42/214, Vietnamese)
G=0.422 (86/204, SGDP_PRJ)
G=0.40 (28/70, Ancient Sardinia)
G=0.50 (20/40, GENOME_DK)
A=0.50 (20/40, GENOME_DK)
G=0.39 (14/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ITPR2 : 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	18888	G=0.54744	A=0.45256
European	Sub	14284	G=0.45863	A=0.54137
African	Sub	2946	G=0.8802	A=0.1198
African Others	Sub	114	G=0.930	A=0.070
African American	Sub	2832	G=0.8782	A=0.1218
Asian	Sub	112	G=0.857	A=0.143
East Asian	Sub	86	G=0.87	A=0.13
Other Asian	Sub	26	G=0.81	A=0.19
Latin American 1	Sub	146	G=0.651	A=0.349
Latin American 2	Sub	610	G=0.749	A=0.251
South Asian	Sub	98	G=0.80	A=0.20
Other	Sub	692	G=0.679	A=0.321

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	G=0.652242	A=0.347758
gnomAD - Genomes	Global	Study-wide	139960	G=0.630723	A=0.369277
gnomAD - Genomes	European	Sub	75782	G=0.48071	A=0.51929
gnomAD - Genomes	African	Sub	41952	G=0.87772	A=0.12228
gnomAD - Genomes	American	Sub	13634	G=0.67053	A=0.32947
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.5970	A=0.4030
gnomAD - Genomes	East Asian	Sub	3128	G=0.8136	A=0.1864
gnomAD - Genomes	Other	Sub	2146	G=0.6323	A=0.3677
14KJPN	JAPANESE	Study-wide	28258	G=0.85296	A=0.14704
Allele Frequency Aggregator	Total	Global	18888	G=0.54744	A=0.45256
Allele Frequency Aggregator	European	Sub	14284	G=0.45863	A=0.54137
Allele Frequency Aggregator	African	Sub	2946	G=0.8802	A=0.1198
Allele Frequency Aggregator	Other	Sub	692	G=0.679	A=0.321
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.749	A=0.251
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.651	A=0.349
Allele Frequency Aggregator	Asian	Sub	112	G=0.857	A=0.143
Allele Frequency Aggregator	South Asian	Sub	98	G=0.80	A=0.20
8.3KJPN	JAPANESE	Study-wide	16760	G=0.85286	A=0.14714
1000Genomes_30x	Global	Study-wide	6404	G=0.7527	A=0.2473
1000Genomes_30x	African	Sub	1786	G=0.9283	A=0.0717
1000Genomes_30x	Europe	Sub	1266	G=0.4423	A=0.5577
1000Genomes_30x	South Asian	Sub	1202	G=0.7879	A=0.2121
1000Genomes_30x	East Asian	Sub	1170	G=0.8085	A=0.1915
1000Genomes_30x	American	Sub	980	G=0.723	A=0.277
1000Genomes	Global	Study-wide	5008	G=0.7544	A=0.2456
1000Genomes	African	Sub	1322	G=0.9297	A=0.0703
1000Genomes	East Asian	Sub	1008	G=0.8115	A=0.1885
1000Genomes	Europe	Sub	1006	G=0.4583	A=0.5417
1000Genomes	South Asian	Sub	978	G=0.786	A=0.214
1000Genomes	American	Sub	694	G=0.722	A=0.278
Genetic variation in the Estonian population	Estonian	Study-wide	4478	G=0.4098	A=0.5902
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.4831	A=0.5169
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.4835	A=0.5165
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8195	A=0.1805
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.493	A=0.507
Northern Sweden	ACPOP	Study-wide	600	G=0.465	A=0.535
HapMap	Global	Study-wide	328	G=0.704	A=0.296
HapMap	African	Sub	120	G=0.892	A=0.108
HapMap	American	Sub	120	G=0.408	A=0.592
HapMap	Asian	Sub	88	G=0.85	A=0.15
Qatari	Global	Study-wide	216	G=0.681	A=0.319
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.804	A=0.196
SGDP_PRJ	Global	Study-wide	204	G=0.422	A=0.578
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	70	G=0.40	A=0.60
The Danish reference pan genome	Danish	Study-wide	40	G=0.50	A=0.50
Siberian	Global	Study-wide	36	G=0.39	A=0.61

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 12	NC_000012.12:g.26769140G>A
GRCh37.p13 chr 12	NC_000012.11:g.26922073G>A
ITPR2 RefSeqGene	NG_042142.1:g.69059C>T

Gene: ITPR2, inositol 1,4,5-trisphosphate receptor type 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ITPR2 transcript variant 1	NM_002223.4:c.163+21017C>T	N/A	Intron Variant
ITPR2 transcript variant X1	XM_017019266.2:c.163+2101… XM_017019266.2:c.163+21017C>T	N/A	Intron Variant
ITPR2 transcript variant X5	XM_017019269.3:c.163+2101… XM_017019269.3:c.163+21017C>T	N/A	Intron Variant
ITPR2 transcript variant X2	XM_047428801.1:c.97+21017… XM_047428801.1:c.97+21017C>T	N/A	Intron Variant
ITPR2 transcript variant X3	XR_001748686.3:n.	N/A	Intron Variant
ITPR2 transcript variant X4	XR_001748687.2: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	G=	A
GRCh38.p14 chr 12	NC_000012.12:g.26769140=	NC_000012.12:g.26769140G>A
GRCh37.p13 chr 12	NC_000012.11:g.26922073=	NC_000012.11:g.26922073G>A
ITPR2 RefSeqGene	NG_042142.1:g.69059=	NG_042142.1:g.69059C>T
ITPR2 transcript	NM_002223.2:c.163+21017=	NM_002223.2:c.163+21017C>T
ITPR2 transcript variant 1	NM_002223.4:c.163+21017=	NM_002223.4:c.163+21017C>T
ITPR2 transcript variant X1	XM_017019266.2:c.163+21017=	XM_017019266.2:c.163+21017C>T
ITPR2 transcript variant X5	XM_017019269.3:c.163+21017=	XM_017019269.3:c.163+21017C>T
ITPR2 transcript variant X2	XM_047428801.1:c.97+21017=	XM_047428801.1:c.97+21017C>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#.

67 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss19951618	Feb 28, 2004 (120)
2	SSAHASNP	ss20880553	Apr 05, 2004 (121)
3	ABI	ss38922761	Mar 14, 2006 (126)
4	HGSV	ss77203583	Dec 07, 2007 (129)
5	HGSV	ss82182134	Dec 16, 2007 (130)
6	BCMHGSC_JDW	ss89047579	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss97296378	Feb 06, 2009 (130)
8	1000GENOMES	ss111683186	Jan 25, 2009 (130)
9	1000GENOMES	ss113323177	Jan 25, 2009 (130)
10	ENSEMBL	ss132106320	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss168013372	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss169396622	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss170622522	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss208236731	Jul 04, 2010 (132)
15	1000GENOMES	ss225666137	Jul 14, 2010 (132)
16	1000GENOMES	ss235871039	Jul 15, 2010 (132)
17	1000GENOMES	ss242439999	Jul 15, 2010 (132)
18	GMI	ss281320813	May 04, 2012 (137)
19	GMI	ss286529607	Apr 25, 2013 (138)
20	PJP	ss291406316	May 09, 2011 (134)
21	TISHKOFF	ss563064991	Apr 25, 2013 (138)
22	SSMP	ss658603760	Apr 25, 2013 (138)
23	EVA-GONL	ss989359266	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1078337750	Aug 21, 2014 (142)
25	1000GENOMES	ss1344360493	Aug 21, 2014 (142)
26	DDI	ss1426880415	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1576180521	Apr 01, 2015 (144)
28	EVA_DECODE	ss1599033442	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1628252365	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1671246398	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1932722041	Feb 12, 2016 (147)
32	JJLAB	ss2027110427	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2155436698	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2188701176	Dec 20, 2016 (150)
35	GRF	ss2699766660	Nov 08, 2017 (151)
36	GNOMAD	ss2908617649	Nov 08, 2017 (151)
37	SWEGEN	ss3009395470	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3027362523	Nov 08, 2017 (151)
39	CSHL	ss3349980959	Nov 08, 2017 (151)
40	ILLUMINA	ss3641027631	Oct 12, 2018 (152)
41	ILLUMINA	ss3641322288	Oct 12, 2018 (152)
42	URBANLAB	ss3649797191	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3676713848	Jul 13, 2019 (153)
44	EVA_DECODE	ss3693338435	Jul 13, 2019 (153)
45	ACPOP	ss3738872812	Jul 13, 2019 (153)
46	EVA	ss3750278764	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3815598265	Jul 13, 2019 (153)
48	EVA	ss3833036699	Apr 26, 2020 (154)
49	EVA	ss3840086822	Apr 26, 2020 (154)
50	EVA	ss3845570873	Apr 26, 2020 (154)
51	SGDP_PRJ	ss3877926348	Apr 26, 2020 (154)
52	KRGDB	ss3926466530	Apr 26, 2020 (154)
53	EVA	ss3985582410	Apr 26, 2021 (155)
54	TOPMED	ss4912592657	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5205571211	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5290200732	Oct 16, 2022 (156)
57	EVA	ss5404629353	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5485049251	Oct 16, 2022 (156)
59	EVA	ss5510632081	Oct 16, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5587325344	Oct 16, 2022 (156)
61	SANFORD_IMAGENETICS	ss5652817456	Oct 16, 2022 (156)
62	TOMMO_GENOMICS	ss5754515669	Oct 16, 2022 (156)
63	YY_MCH	ss5813113300	Oct 16, 2022 (156)
64	EVA	ss5837744385	Oct 16, 2022 (156)
65	EVA	ss5850309250	Oct 16, 2022 (156)
66	EVA	ss5903731098	Oct 16, 2022 (156)
67	EVA	ss5944172720	Oct 16, 2022 (156)
68	1000Genomes	NC_000012.11 - 26922073	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000012.12 - 26769140	Oct 16, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 26922073	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000012.11 - 26922073	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000012.11 - 26922073	Apr 26, 2020 (154)
73	gnomAD - Genomes	NC_000012.12 - 26769140	Apr 26, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000012.11 - 26922073	Apr 26, 2020 (154)
75	HapMap	NC_000012.12 - 26769140	Apr 26, 2020 (154)
76	KOREAN population from KRGDB	NC_000012.11 - 26922073	Apr 26, 2020 (154)
77	Northern Sweden	NC_000012.11 - 26922073	Jul 13, 2019 (153)
78	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000012.11 - 26922073	Apr 26, 2021 (155)
79	Qatari	NC_000012.11 - 26922073	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000012.11 - 26922073	Apr 26, 2020 (154)
81	Siberian	NC_000012.11 - 26922073	Apr 26, 2020 (154)
82	8.3KJPN	NC_000012.11 - 26922073	Apr 26, 2021 (155)
83	14KJPN	NC_000012.12 - 26769140	Oct 16, 2022 (156)
84	TopMed	NC_000012.12 - 26769140	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000012.11 - 26922073	Oct 12, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000012.11 - 26922073	Jul 13, 2019 (153)
87	ALFA	NC_000012.12 - 26769140	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)
rs61197370	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77203583, ss82182134	NC_000012.9:26813339:G:A	NC_000012.12:26769139:G:A	(self)
ss89047579, ss111683186, ss113323177, ss168013372, ss169396622, ss170622522, ss208236731, ss281320813, ss286529607, ss291406316, ss1599033442	NC_000012.10:26813339:G:A	NC_000012.12:26769139:G:A	(self)
57085447, 31702082, 22452096, 2894185, 14144703, 33643924, 12157677, 808337, 14763971, 29943328, 7953052, 63540518, 31702082, 7034841, ss225666137, ss235871039, ss242439999, ss563064991, ss658603760, ss989359266, ss1078337750, ss1344360493, ss1426880415, ss1576180521, ss1628252365, ss1671246398, ss1932722041, ss2027110427, ss2155436698, ss2699766660, ss2908617649, ss3009395470, ss3349980959, ss3641027631, ss3641322288, ss3676713848, ss3738872812, ss3750278764, ss3833036699, ss3840086822, ss3877926348, ss3926466530, ss3985582410, ss5205571211, ss5404629353, ss5510632081, ss5652817456, ss5837744385, ss5944172720	NC_000012.11:26922072:G:A	NC_000012.12:26769139:G:A	(self)
74851279, 402519384, 780958, 88352773, 128138314, 6075360795, ss2188701176, ss3027362523, ss3649797191, ss3693338435, ss3815598265, ss3845570873, ss4912592657, ss5290200732, ss5485049251, ss5587325344, ss5754515669, ss5813113300, ss5850309250, ss5903731098	NC_000012.12:26769139:G:A	NC_000012.12:26769139:G:A	(self)
ss19951618, ss20880553	NT_009714.16:19681046:G:A	NC_000012.12:26769139:G:A	(self)
ss38922761, ss97296378, ss132106320	NT_009714.17:19682196:G:A	NC_000012.12:26769139:G:A	(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 rs12582043

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

rs12582043