Name: rs76956075
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.

rs76956075

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:26704832 (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: A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.035649 (9436/264690, TOPMED)
T=0.037083 (5200/140226, GnomAD)
T=0.03001 (2362/78698, PAGE_STUDY) (+ 10 more)
T=0.03891 (735/18890, ALFA)
T=0.0222 (142/6404, 1000G_30x)
T=0.0214 (107/5008, 1000G)
T=0.0400 (179/4480, Estonian)
T=0.0451 (174/3854, ALSPAC)
T=0.0388 (144/3708, TWINSUK)
T=0.047 (47/998, GoNL)
T=0.035 (21/600, NorthernSweden)
T=0.069 (15/216, Qatari)
A=0.46 (13/28, SGDP_PRJ)

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	18890	A=0.96109	T=0.03891
European	Sub	14286	A=0.96087	T=0.03913
African	Sub	2946	A=0.9542	T=0.0458
African Others	Sub	114	A=0.965	T=0.035
African American	Sub	2832	A=0.9537	T=0.0463
Asian	Sub	112	A=1.000	T=0.000
East Asian	Sub	86	A=1.00	T=0.00
Other Asian	Sub	26	A=1.00	T=0.00
Latin American 1	Sub	146	A=0.966	T=0.034
Latin American 2	Sub	610	A=0.985	T=0.015
South Asian	Sub	98	A=1.00	T=0.00
Other	Sub	692	A=0.961	T=0.039

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	A=0.964351	T=0.035649
gnomAD - Genomes	Global	Study-wide	140226	A=0.962917	T=0.037083
gnomAD - Genomes	European	Sub	75938	A=0.96215	T=0.03785
gnomAD - Genomes	African	Sub	42038	A=0.95913	T=0.04087
gnomAD - Genomes	American	Sub	13648	A=0.97267	T=0.02733
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.9539	T=0.0461
gnomAD - Genomes	East Asian	Sub	3126	A=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2154	A=0.9624	T=0.0376
The PAGE Study	Global	Study-wide	78698	A=0.96999	T=0.03001
The PAGE Study	AfricanAmerican	Sub	32516	A=0.96082	T=0.03918
The PAGE Study	Mexican	Sub	10810	A=0.97660	T=0.02340
The PAGE Study	Asian	Sub	8316	A=0.9995	T=0.0005
The PAGE Study	PuertoRican	Sub	7918	A=0.9649	T=0.0351
The PAGE Study	NativeHawaiian	Sub	4534	A=0.9859	T=0.0141
The PAGE Study	Cuban	Sub	4228	A=0.9591	T=0.0409
The PAGE Study	Dominican	Sub	3828	A=0.9579	T=0.0421
The PAGE Study	CentralAmerican	Sub	2450	A=0.9767	T=0.0233
The PAGE Study	SouthAmerican	Sub	1982	A=0.9753	T=0.0247
The PAGE Study	NativeAmerican	Sub	1260	A=0.9627	T=0.0373
The PAGE Study	SouthAsian	Sub	856	A=0.998	T=0.002
Allele Frequency Aggregator	Total	Global	18890	A=0.96109	T=0.03891
Allele Frequency Aggregator	European	Sub	14286	A=0.96087	T=0.03913
Allele Frequency Aggregator	African	Sub	2946	A=0.9542	T=0.0458
Allele Frequency Aggregator	Other	Sub	692	A=0.961	T=0.039
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.985	T=0.015
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.966	T=0.034
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	T=0.00
1000Genomes_30x	Global	Study-wide	6404	A=0.9778	T=0.0222
1000Genomes_30x	African	Sub	1786	A=0.9630	T=0.0370
1000Genomes_30x	Europe	Sub	1266	A=0.9613	T=0.0387
1000Genomes_30x	South Asian	Sub	1202	A=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	A=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	A=0.973	T=0.027
1000Genomes	Global	Study-wide	5008	A=0.9786	T=0.0214
1000Genomes	African	Sub	1322	A=0.9644	T=0.0356
1000Genomes	East Asian	Sub	1008	A=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	A=0.9592	T=0.0408
1000Genomes	South Asian	Sub	978	A=1.000	T=0.000
1000Genomes	American	Sub	694	A=0.974	T=0.026
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9600	T=0.0400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9549	T=0.0451
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9612	T=0.0388
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.953	T=0.047
Northern Sweden	ACPOP	Study-wide	600	A=0.965	T=0.035
Qatari	Global	Study-wide	216	A=0.931	T=0.069
SGDP_PRJ	Global	Study-wide	28	A=0.46	T=0.54

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.26704832A>T
GRCh37.p13 chr 12	NC_000012.11:g.26857765A>T
ITPR2 RefSeqGene	NG_042142.1:g.133367T>A

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.951+6341T>A	N/A	Intron Variant
ITPR2 transcript variant X1	XM_017019266.2:c.952-3601… XM_017019266.2:c.952-3601T>A	N/A	Intron Variant
ITPR2 transcript variant X5	XM_017019269.3:c.952-3601… XM_017019269.3:c.952-3601T>A	N/A	Intron Variant
ITPR2 transcript variant X2	XM_047428801.1:c.886-3601… XM_047428801.1:c.886-3601T>A	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	A=	T
GRCh38.p14 chr 12	NC_000012.12:g.26704832=	NC_000012.12:g.26704832A>T
GRCh37.p13 chr 12	NC_000012.11:g.26857765=	NC_000012.11:g.26857765A>T
ITPR2 RefSeqGene	NG_042142.1:g.133367=	NG_042142.1:g.133367T>A
ITPR2 transcript	NM_002223.2:c.951+6341=	NM_002223.2:c.951+6341T>A
ITPR2 transcript variant 1	NM_002223.4:c.951+6341=	NM_002223.4:c.951+6341T>A
ITPR2 transcript variant X1	XM_017019266.2:c.952-3601=	XM_017019266.2:c.952-3601T>A
ITPR2 transcript variant X5	XM_017019269.3:c.952-3601=	XM_017019269.3:c.952-3601T>A
ITPR2 transcript variant X2	XM_047428801.1:c.886-3601=	XM_047428801.1:c.886-3601T>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#.

38 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss225665921	Jul 14, 2010 (132)
2	1000GENOMES	ss235870837	Jul 15, 2010 (132)
3	TISHKOFF	ss563064734	Apr 25, 2013 (138)
4	EVA-GONL	ss989358823	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1078337429	Aug 21, 2014 (142)
6	1000GENOMES	ss1344358897	Aug 21, 2014 (142)
7	EVA_DECODE	ss1599032988	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1628251440	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1671245473	Apr 01, 2015 (144)
10	HAMMER_LAB	ss1807170705	Sep 08, 2015 (146)
11	WEILL_CORNELL_DGM	ss1932721690	Feb 12, 2016 (147)
12	ILLUMINA	ss1959422956	Feb 12, 2016 (147)
13	JJLAB	ss2027110213	Sep 14, 2016 (149)
14	HUMAN_LONGEVITY	ss2188697824	Dec 20, 2016 (150)
15	GNOMAD	ss2908613176	Nov 08, 2017 (151)
16	SWEGEN	ss3009394863	Nov 08, 2017 (151)
17	ILLUMINA	ss3021416894	Nov 08, 2017 (151)
18	CSHL	ss3349980781	Nov 08, 2017 (151)
19	ILLUMINA	ss3651791343	Oct 12, 2018 (152)
20	EGCUT_WGS	ss3676713185	Jul 13, 2019 (153)
21	EVA_DECODE	ss3693337703	Jul 13, 2019 (153)
22	ILLUMINA	ss3725312870	Jul 13, 2019 (153)
23	ACPOP	ss3738872466	Jul 13, 2019 (153)
24	PAGE_CC	ss3771681954	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3815597794	Jul 13, 2019 (153)
26	EVA	ss3840086678	Apr 26, 2020 (154)
27	EVA	ss3845570728	Apr 26, 2020 (154)
28	SGDP_PRJ	ss3877925575	Apr 26, 2020 (154)
29	TOPMED	ss4912578407	Apr 26, 2021 (155)
30	1000G_HIGH_COVERAGE	ss5290199410	Oct 16, 2022 (156)
31	EVA	ss5404626785	Oct 16, 2022 (156)
32	HUGCELL_USP	ss5485048045	Oct 16, 2022 (156)
33	EVA	ss5510631896	Oct 16, 2022 (156)
34	1000G_HIGH_COVERAGE	ss5587323295	Oct 16, 2022 (156)
35	SANFORD_IMAGENETICS	ss5652816780	Oct 16, 2022 (156)
36	EVA	ss5837743870	Oct 16, 2022 (156)
37	EVA	ss5903729444	Oct 16, 2022 (156)
38	EVA	ss5944171898	Oct 16, 2022 (156)
39	1000Genomes	NC_000012.11 - 26857765	Oct 12, 2018 (152)
40	1000Genomes_30x	NC_000012.12 - 26704832	Oct 16, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 26857765	Oct 12, 2018 (152)
42	Genetic variation in the Estonian population	NC_000012.11 - 26857765	Oct 12, 2018 (152)
43	gnomAD - Genomes	NC_000012.12 - 26704832	Apr 26, 2021 (155)
44	Genome of the Netherlands Release 5	NC_000012.11 - 26857765	Apr 26, 2020 (154)
45	Northern Sweden	NC_000012.11 - 26857765	Jul 13, 2019 (153)
46	The PAGE Study	NC_000012.12 - 26704832	Jul 13, 2019 (153)
47	Qatari	NC_000012.11 - 26857765	Apr 26, 2020 (154)
48	SGDP_PRJ	NC_000012.11 - 26857765	Apr 26, 2020 (154)
49	TopMed	NC_000012.12 - 26704832	Apr 26, 2021 (155)
50	UK 10K study - Twins	NC_000012.11 - 26857765	Oct 12, 2018 (152)
51	ALFA	NC_000012.12 - 26704832	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1599032988	NC_000012.10:26749031:A:T	NC_000012.12:26704831:A:T	(self)
57083800, 31701084, 22451433, 14144268, 12157331, 14763620, 29942555, 31701084, ss225665921, ss235870837, ss563064734, ss989358823, ss1078337429, ss1344358897, ss1628251440, ss1671245473, ss1807170705, ss1932721690, ss1959422956, ss2027110213, ss2908613176, ss3009394863, ss3021416894, ss3349980781, ss3651791343, ss3676713185, ss3738872466, ss3840086678, ss3877925575, ss5404626785, ss5510631896, ss5652816780, ss5837743870, ss5944171898	NC_000012.11:26857764:A:T	NC_000012.12:26704831:A:T	(self)
74849230, 402508172, 903423, 128124064, 6860349113, ss2188697824, ss3693337703, ss3725312870, ss3771681954, ss3815597794, ss3845570728, ss4912578407, ss5290199410, ss5485048045, ss5587323295, ss5903729444	NC_000012.12:26704831:A:T	NC_000012.12:26704831:A: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 rs76956075

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

rs76956075