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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.

rs10212373

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:4720765 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.312399 (82689/264690, TOPMED)
T=0.10082 (2849/28258, 14KJPN)
T=0.10014 (1678/16756, 8.3KJPN) (+ 13 more)
T=0.30760 (4841/15738, ALFA)
T=0.1807 (1157/6404, 1000G_30x)
T=0.1801 (902/5008, 1000G)
T=0.4154 (1861/4480, Estonian)
T=0.0979 (286/2922, KOREAN)
T=0.1174 (215/1832, Korea1K)
C=0.482 (481/998, GoNL)
T=0.460 (276/600, NorthernSweden)
C=0.413 (95/230, SGDP_PRJ)
T=0.199 (43/216, Qatari)
T=0.075 (16/214, Vietnamese)
C=0.47 (19/40, GENOME_DK)
C=0.38 (12/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ITPR1 : 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 15832 C=0.69233 G=0.00000, T=0.30767
European Sub 12968 C=0.63109 G=0.00000, T=0.36891
African Sub 1710 C=1.0000 G=0.0000, T=0.0000
African Others Sub 68 C=1.00 G=0.00, T=0.00
African American Sub 1642 C=1.0000 G=0.0000, T=0.0000
Asian Sub 88 C=1.00 G=0.00, T=0.00
East Asian Sub 68 C=1.00 G=0.00, T=0.00
Other Asian Sub 20 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 68 C=1.00 G=0.00, T=0.00
Latin American 2 Sub 350 C=1.000 G=0.000, T=0.000
South Asian Sub 68 C=1.00 G=0.00, T=0.00
Other Sub 580 C=0.850 G=0.000, T=0.150


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 264690 C=0.687601 T=0.312399
14KJPN JAPANESE Study-wide 28258 C=0.89918 T=0.10082
8.3KJPN JAPANESE Study-wide 16756 C=0.89986 T=0.10014
Allele Frequency Aggregator Total Global 15738 C=0.69240 G=0.00000, T=0.30760
Allele Frequency Aggregator European Sub 12892 C=0.63070 G=0.00000, T=0.36930
Allele Frequency Aggregator African Sub 1710 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 562 C=0.858 G=0.000, T=0.142
Allele Frequency Aggregator Latin American 2 Sub 350 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 88 C=1.00 G=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 68 C=1.00 G=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 68 C=1.00 G=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.7800 G=0.0394, T=0.1807
1000Genomes_30x African Sub 1786 C=0.8024 G=0.1344, T=0.0633
1000Genomes_30x Europe Sub 1266 C=0.5806 G=0.0008, T=0.4186
1000Genomes_30x South Asian Sub 1202 C=0.8777 G=0.0000, T=0.1223
1000Genomes_30x East Asian Sub 1170 C=0.9145 G=0.0000, T=0.0855
1000Genomes_30x American Sub 980 C=0.716 G=0.011, T=0.272
1000Genomes Global Study-wide 5008 C=0.7837 G=0.0361, T=0.1801
1000Genomes African Sub 1322 C=0.8056 G=0.1286, T=0.0658
1000Genomes East Asian Sub 1008 C=0.9097 G=0.0000, T=0.0903
1000Genomes Europe Sub 1006 C=0.5736 G=0.0010, T=0.4254
1000Genomes South Asian Sub 978 C=0.881 G=0.000, T=0.119
1000Genomes American Sub 694 C=0.726 G=0.014, T=0.259
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5846 T=0.4154
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9021 T=0.0979
Korean Genome Project KOREAN Study-wide 1832 C=0.8826 T=0.1174
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.482 T=0.518
Northern Sweden ACPOP Study-wide 600 C=0.540 T=0.460
SGDP_PRJ Global Study-wide 230 C=0.413 G=0.074, T=0.513
Qatari Global Study-wide 216 C=0.801 T=0.199
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.925 T=0.075
The Danish reference pan genome Danish Study-wide 40 C=0.47 T=0.53
Siberian Global Study-wide 32 C=0.38 T=0.62
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.p14 chr 3 NC_000003.12:g.4720765C>G
GRCh38.p14 chr 3 NC_000003.12:g.4720765C>T
GRCh37.p13 chr 3 NC_000003.11:g.4762449C>G
GRCh37.p13 chr 3 NC_000003.11:g.4762449C>T
ITPR1 RefSeqGene NG_016144.1:g.232418C>G
ITPR1 RefSeqGene NG_016144.1:g.232418C>T
Gene: ITPR1, inositol 1,4,5-trisphosphate receptor type 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ITPR1 transcript variant 1 NM_001099952.4:c.5076+889…

NM_001099952.4:c.5076+8897C>G

N/A Intron Variant
ITPR1 transcript variant 3 NM_001168272.2:c.5091+336…

NM_001168272.2:c.5091+3366C>G

N/A Intron Variant
ITPR1 transcript variant 4 NM_001378452.1:c.5136+336…

NM_001378452.1:c.5136+3366C>G

N/A Intron Variant
ITPR1 transcript variant 2 NM_002222.7:c.5031+8897C>G N/A Intron 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.

Not Reported in ClinVar
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 C= G T
GRCh38.p14 chr 3 NC_000003.12:g.4720765= NC_000003.12:g.4720765C>G NC_000003.12:g.4720765C>T
GRCh37.p13 chr 3 NC_000003.11:g.4762449= NC_000003.11:g.4762449C>G NC_000003.11:g.4762449C>T
ITPR1 RefSeqGene NG_016144.1:g.232418= NG_016144.1:g.232418C>G NG_016144.1:g.232418C>T
ITPR1 transcript variant 1 NM_001099952.2:c.5076+8897= NM_001099952.2:c.5076+8897C>G NM_001099952.2:c.5076+8897C>T
ITPR1 transcript variant 1 NM_001099952.4:c.5076+8897= NM_001099952.4:c.5076+8897C>G NM_001099952.4:c.5076+8897C>T
ITPR1 transcript variant 3 NM_001168272.1:c.5091+3366= NM_001168272.1:c.5091+3366C>G NM_001168272.1:c.5091+3366C>T
ITPR1 transcript variant 3 NM_001168272.2:c.5091+3366= NM_001168272.2:c.5091+3366C>G NM_001168272.2:c.5091+3366C>T
ITPR1 transcript variant 4 NM_001378452.1:c.5136+3366= NM_001378452.1:c.5136+3366C>G NM_001378452.1:c.5136+3366C>T
ITPR1 transcript variant 2 NM_002222.5:c.5031+8897= NM_002222.5:c.5031+8897C>G NM_002222.5:c.5031+8897C>T
ITPR1 transcript variant 2 NM_002222.7:c.5031+8897= NM_002222.7:c.5031+8897C>G NM_002222.7:c.5031+8897C>T
ITPR1 transcript variant X1 XM_005265108.1:c.5136+3366= XM_005265108.1:c.5136+3366C>G XM_005265108.1:c.5136+3366C>T
ITPR1 transcript variant X2 XM_005265109.1:c.5104-6361= XM_005265109.1:c.5104-6361C>G XM_005265109.1:c.5104-6361C>T
ITPR1 transcript variant X3 XM_005265110.1:c.5103+8897= XM_005265110.1:c.5103+8897C>G XM_005265110.1:c.5103+8897C>T
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#.

67 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 WUGSC_SSAHASNP ss14077852 Dec 05, 2003 (119)
2 ABI ss44406071 Mar 14, 2006 (126)
3 HGSV ss78774301 Dec 06, 2007 (129)
4 HUMANGENOME_JCVI ss95980439 Feb 03, 2009 (130)
5 1000GENOMES ss111158826 Jan 25, 2009 (130)
6 ILLUMINA-UK ss116952788 Feb 14, 2009 (130)
7 ENSEMBL ss135314283 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss161901534 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss205992597 Jul 04, 2010 (132)
10 1000GENOMES ss219948950 Jul 14, 2010 (132)
11 1000GENOMES ss231684580 Jul 14, 2010 (132)
12 1000GENOMES ss239122928 Jul 15, 2010 (132)
13 GMI ss276990897 May 04, 2012 (137)
14 GMI ss284583808 Apr 25, 2013 (138)
15 TISHKOFF ss556387018 Apr 25, 2013 (138)
16 SSMP ss650050760 Apr 25, 2013 (138)
17 EVA-GONL ss978212672 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1070129522 Aug 21, 2014 (142)
19 1000GENOMES ss1302583498 Aug 21, 2014 (142)
20 1000GENOMES ss1302583499 Aug 21, 2014 (142)
21 DDI ss1429312122 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1579820906 Apr 01, 2015 (144)
23 EVA_DECODE ss1587672487 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1606297218 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1606297219 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1649291251 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1649291252 Apr 01, 2015 (144)
28 HAMMER_LAB ss1798767850 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1921464892 Feb 12, 2016 (147)
30 GENOMED ss1969308744 Jul 19, 2016 (147)
31 CSHL ss2136688389 Nov 08, 2017 (151)
32 USC_VALOUEV ss2149350914 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2248641627 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2625141626 Nov 08, 2017 (151)
35 GRF ss2704707863 Nov 08, 2017 (151)
36 GNOMAD ss2788935840 Nov 08, 2017 (151)
37 AFFY ss2985245242 Nov 08, 2017 (151)
38 AFFY ss2985862047 Nov 08, 2017 (151)
39 SWEGEN ss2991742743 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3024403740 Nov 08, 2017 (151)
41 CSHL ss3344857414 Nov 08, 2017 (151)
42 URBANLAB ss3647328788 Oct 11, 2018 (152)
43 ILLUMINA ss3654013704 Oct 11, 2018 (152)
44 EGCUT_WGS ss3659640165 Jul 13, 2019 (153)
45 ACPOP ss3729583704 Jul 13, 2019 (153)
46 EVA ss3759591238 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3802742251 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3802742252 Jul 13, 2019 (153)
49 EVA ss3827632174 Apr 25, 2020 (154)
50 EVA ss3837237434 Apr 25, 2020 (154)
51 EVA ss3842660987 Apr 25, 2020 (154)
52 SGDP_PRJ ss3855108743 Apr 25, 2020 (154)
53 KRGDB ss3900874469 Apr 25, 2020 (154)
54 KOGIC ss3950559463 Apr 25, 2020 (154)
55 TOPMED ss4552429531 Apr 27, 2021 (155)
56 TOMMO_GENOMICS ss5157559351 Apr 27, 2021 (155)
57 1000G_HIGH_COVERAGE ss5252858115 Oct 13, 2022 (156)
58 1000G_HIGH_COVERAGE ss5252858116 Oct 13, 2022 (156)
59 HUGCELL_USP ss5452381069 Oct 13, 2022 (156)
60 HUGCELL_USP ss5452381070 Oct 13, 2022 (156)
61 1000G_HIGH_COVERAGE ss5530597657 Oct 13, 2022 (156)
62 SANFORD_IMAGENETICS ss5631431089 Oct 13, 2022 (156)
63 TOMMO_GENOMICS ss5688759762 Oct 13, 2022 (156)
64 YY_MCH ss5803432176 Oct 13, 2022 (156)
65 EVA ss5825271093 Oct 13, 2022 (156)
66 EVA ss5853465381 Oct 13, 2022 (156)
67 EVA ss5959687564 Oct 13, 2022 (156)
68 1000Genomes NC_000003.11 - 4762449 Oct 11, 2018 (152)
69 1000Genomes_30x NC_000003.12 - 4720765 Oct 13, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 7603887 (NC_000003.11:4762448:C:C 2031/3854, NC_000003.11:4762448:C:T 1823/3854)
Row 7603888 (NC_000003.11:4762448:C:C 3853/3854, NC_000003.11:4762448:C:G 1/3854)

- Oct 11, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 7603887 (NC_000003.11:4762448:C:C 2031/3854, NC_000003.11:4762448:C:T 1823/3854)
Row 7603888 (NC_000003.11:4762448:C:C 3853/3854, NC_000003.11:4762448:C:G 1/3854)

- Oct 11, 2018 (152)
72 Genetic variation in the Estonian population NC_000003.11 - 4762449 Oct 11, 2018 (152)
73 The Danish reference pan genome NC_000003.11 - 4762449 Apr 25, 2020 (154)
74 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 97527765 (NC_000003.12:4720764:C:G 4928/139312)
Row 97527766 (NC_000003.12:4720764:C:T 45865/139286)

- Apr 27, 2021 (155)
75 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 97527765 (NC_000003.12:4720764:C:G 4928/139312)
Row 97527766 (NC_000003.12:4720764:C:T 45865/139286)

- Apr 27, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000003.11 - 4762449 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000003.11 - 4762449 Apr 25, 2020 (154)
78 Korean Genome Project NC_000003.12 - 4720765 Apr 25, 2020 (154)
79 Northern Sweden NC_000003.11 - 4762449 Jul 13, 2019 (153)
80 Qatari NC_000003.11 - 4762449 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000003.11 - 4762449 Apr 25, 2020 (154)
82 Siberian NC_000003.11 - 4762449 Apr 25, 2020 (154)
83 8.3KJPN NC_000003.11 - 4762449 Apr 27, 2021 (155)
84 14KJPN NC_000003.12 - 4720765 Oct 13, 2022 (156)
85 TopMed NC_000003.12 - 4720765 Apr 27, 2021 (155)
86 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 7603887 (NC_000003.11:4762448:C:C 1911/3708, NC_000003.11:4762448:C:T 1797/3708)
Row 7603888 (NC_000003.11:4762448:C:C 3708/3708, NC_000003.11:4762448:C:G 0/3708)

- Oct 11, 2018 (152)
87 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 7603887 (NC_000003.11:4762448:C:C 1911/3708, NC_000003.11:4762448:C:T 1797/3708)
Row 7603888 (NC_000003.11:4762448:C:C 3708/3708, NC_000003.11:4762448:C:G 0/3708)

- Oct 11, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000003.11 - 4762449 Jul 13, 2019 (153)
89 ALFA NC_000003.12 - 4720765 Apr 27, 2021 (155)
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).

Associated ID History Updated (Build)
rs117682155 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
13721271, 7125723, ss556387018, ss1302583498, ss1606297219, ss1649291252, ss1798767850, ss2788935840, ss3855108743, ss5631431089 NC_000003.11:4762448:C:G NC_000003.12:4720764:C:G (self)
18123592, 3221138969, ss2248641627, ss3802742252, ss5252858115, ss5452381070, ss5530597657 NC_000003.12:4720764:C:G NC_000003.12:4720764:C:G (self)
ss78774301 NC_000003.9:4737448:C:T NC_000003.12:4720764:C:T (self)
ss111158826, ss116952788, ss161901534, ss205992597, ss276990897, ss284583808, ss1587672487, ss2136688389 NC_000003.10:4737448:C:T NC_000003.12:4720764:C:T (self)
13721271, 5378413, 5985845, 3336880, 8051863, 2868569, 3506822, 7125723, 1867268, 15528658, 1654452, ss219948950, ss231684580, ss239122928, ss650050760, ss978212672, ss1070129522, ss1302583499, ss1429312122, ss1579820906, ss1606297218, ss1649291251, ss1921464892, ss1969308744, ss2149350914, ss2625141626, ss2704707863, ss2788935840, ss2985245242, ss2985862047, ss2991742743, ss3344857414, ss3654013704, ss3659640165, ss3729583704, ss3759591238, ss3827632174, ss3837237434, ss3855108743, ss3900874469, ss5157559351, ss5631431089, ss5825271093, ss5959687564 NC_000003.11:4762448:C:T NC_000003.12:4720764:C:T (self)
18123592, 6937464, 22596866, 389807086, 3221138969, ss2248641627, ss3024403740, ss3647328788, ss3802742251, ss3842660987, ss3950559463, ss4552429531, ss5252858116, ss5452381069, ss5530597657, ss5688759762, ss5803432176, ss5853465381 NC_000003.12:4720764:C:T NC_000003.12:4720764:C:T (self)
ss14077852 NT_022517.16:4702448:C:T NC_000003.12:4720764:C:T (self)
ss44406071, ss95980439, ss135314283 NT_022517.18:4702448:C:T NC_000003.12:4720764:C:T (self)
Help

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

No publications for rs10212373

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.post761+d5e8e07