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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.

rs723490

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:143969919 (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=0.437251 (115736/264690, TOPMED)
C=0.442626 (61756/139522, GnomAD)
C=0.44048 (12447/28258, 14KJPN) (+ 15 more)
C=0.49667 (11937/24034, ALFA)
C=0.43872 (7353/16760, 8.3KJPN)
C=0.4080 (2613/6404, 1000G_30x)
C=0.4073 (2040/5008, 1000G)
T=0.4449 (1993/4480, Estonian)
C=0.4218 (1236/2930, KOREAN)
C=0.3381 (635/1878, HapMap)
C=0.4514 (827/1832, Korea1K)
T=0.426 (425/998, GoNL)
T=0.460 (276/600, NorthernSweden)
C=0.278 (118/424, SGDP_PRJ)
C=0.440 (95/216, Qatari)
C=0.462 (98/212, Vietnamese)
T=0.45 (18/40, GENOME_DK)
C=0.28 (9/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DIPK2A : 2KB Upstream 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 24034 C=0.49667 T=0.50333
European Sub 18110 C=0.56372 T=0.43628
African Sub 4090 C=0.2024 T=0.7976
African Others Sub 148 C=0.162 T=0.838
African American Sub 3942 C=0.2040 T=0.7960
Asian Sub 120 C=0.317 T=0.683
East Asian Sub 94 C=0.32 T=0.68
Other Asian Sub 26 C=0.31 T=0.69
Latin American 1 Sub 160 C=0.456 T=0.544
Latin American 2 Sub 664 C=0.557 T=0.443
South Asian Sub 98 C=0.57 T=0.43
Other Sub 792 C=0.458 T=0.542


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=0.437251 T=0.562749
gnomAD - Genomes Global Study-wide 139522 C=0.442626 T=0.557374
gnomAD - Genomes European Sub 75610 C=0.55994 T=0.44006
gnomAD - Genomes African Sub 41736 C=0.20265 T=0.79735
gnomAD - Genomes American Sub 13608 C=0.49052 T=0.50948
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.5763 T=0.4237
gnomAD - Genomes East Asian Sub 3112 C=0.4499 T=0.5501
gnomAD - Genomes Other Sub 2138 C=0.4556 T=0.5444
14KJPN JAPANESE Study-wide 28258 C=0.44048 T=0.55952
Allele Frequency Aggregator Total Global 24034 C=0.49667 T=0.50333
Allele Frequency Aggregator European Sub 18110 C=0.56372 T=0.43628
Allele Frequency Aggregator African Sub 4090 C=0.2024 T=0.7976
Allele Frequency Aggregator Other Sub 792 C=0.458 T=0.542
Allele Frequency Aggregator Latin American 2 Sub 664 C=0.557 T=0.443
Allele Frequency Aggregator Latin American 1 Sub 160 C=0.456 T=0.544
Allele Frequency Aggregator Asian Sub 120 C=0.317 T=0.683
Allele Frequency Aggregator South Asian Sub 98 C=0.57 T=0.43
8.3KJPN JAPANESE Study-wide 16760 C=0.43872 T=0.56128
1000Genomes_30x Global Study-wide 6404 C=0.4080 T=0.5920
1000Genomes_30x African Sub 1786 C=0.1405 T=0.8595
1000Genomes_30x Europe Sub 1266 C=0.5245 T=0.4755
1000Genomes_30x South Asian Sub 1202 C=0.4908 T=0.5092
1000Genomes_30x East Asian Sub 1170 C=0.4846 T=0.5154
1000Genomes_30x American Sub 980 C=0.552 T=0.448
1000Genomes Global Study-wide 5008 C=0.4073 T=0.5927
1000Genomes African Sub 1322 C=0.1437 T=0.8563
1000Genomes East Asian Sub 1008 C=0.4742 T=0.5258
1000Genomes Europe Sub 1006 C=0.5119 T=0.4881
1000Genomes South Asian Sub 978 C=0.488 T=0.512
1000Genomes American Sub 694 C=0.548 T=0.452
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5551 T=0.4449
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.4218 A=0.0000, G=0.0000, T=0.5782
HapMap Global Study-wide 1878 C=0.3381 T=0.6619
HapMap American Sub 764 C=0.486 T=0.514
HapMap African Sub 692 C=0.113 T=0.887
HapMap Asian Sub 250 C=0.412 T=0.588
HapMap Europe Sub 172 C=0.483 T=0.517
Korean Genome Project KOREAN Study-wide 1832 C=0.4514 T=0.5486
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.574 T=0.426
Northern Sweden ACPOP Study-wide 600 C=0.540 T=0.460
SGDP_PRJ Global Study-wide 424 C=0.278 T=0.722
Qatari Global Study-wide 216 C=0.440 T=0.560
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.462 T=0.538
The Danish reference pan genome Danish Study-wide 40 C=0.55 T=0.45
Siberian Global Study-wide 32 C=0.28 T=0.72
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.143969919C>A
GRCh38.p14 chr 3 NC_000003.12:g.143969919C>G
GRCh38.p14 chr 3 NC_000003.12:g.143969919C>T
GRCh37.p13 chr 3 NC_000003.11:g.143688761C>A
GRCh37.p13 chr 3 NC_000003.11:g.143688761C>G
GRCh37.p13 chr 3 NC_000003.11:g.143688761C>T
Gene: DIPK2A, divergent protein kinase domain 2A (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DIPK2A transcript variant 3 NM_001363944.1:c. N/A Upstream Transcript Variant
DIPK2A transcript variant 1 NM_173552.5:c. N/A Upstream Transcript Variant
DIPK2A transcript variant 2 NM_001134470.2:c. N/A N/A
DIPK2A transcript variant X1 XM_011512543.3:c. N/A Upstream Transcript 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= A G T
GRCh38.p14 chr 3 NC_000003.12:g.143969919= NC_000003.12:g.143969919C>A NC_000003.12:g.143969919C>G NC_000003.12:g.143969919C>T
GRCh37.p13 chr 3 NC_000003.11:g.143688761= NC_000003.11:g.143688761C>A NC_000003.11:g.143688761C>G NC_000003.11:g.143688761C>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#.

80 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss65736 Oct 05, 2000 (86)
2 SC_JCM ss5936333 Feb 20, 2003 (111)
3 SSAHASNP ss21956946 Apr 05, 2004 (121)
4 ABI ss44418908 Mar 14, 2006 (126)
5 ILLUMINA ss65719615 Oct 16, 2006 (127)
6 ILLUMINA ss74855114 Dec 06, 2007 (129)
7 HGSV ss79081322 Dec 06, 2007 (129)
8 BCMHGSC_JDW ss92309487 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss96059062 Feb 04, 2009 (130)
10 BGI ss106303337 Feb 04, 2009 (130)
11 1000GENOMES ss111056143 Jan 25, 2009 (130)
12 1000GENOMES ss112536284 Jan 25, 2009 (130)
13 ILLUMINA-UK ss117304678 Feb 14, 2009 (130)
14 KRIBB_YJKIM ss119364680 Dec 01, 2009 (131)
15 ILLUMINA ss120245563 Dec 01, 2009 (131)
16 ENSEMBL ss133143558 Dec 01, 2009 (131)
17 ENSEMBL ss139201823 Dec 01, 2009 (131)
18 GMI ss156291975 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss162683246 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss164481359 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss167280358 Jul 04, 2010 (132)
22 ILLUMINA ss174303020 Jul 04, 2010 (132)
23 BUSHMAN ss203291697 Jul 04, 2010 (132)
24 1000GENOMES ss220473282 Jul 14, 2010 (132)
25 1000GENOMES ss232065356 Jul 14, 2010 (132)
26 1000GENOMES ss239430166 Jul 15, 2010 (132)
27 ILLUMINA ss244256423 Jul 04, 2010 (132)
28 GMI ss277382996 May 04, 2012 (137)
29 SSMP ss650726859 Apr 25, 2013 (138)
30 EVA-GONL ss979251374 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1070897980 Aug 21, 2014 (142)
32 1000GENOMES ss1306512927 Aug 21, 2014 (142)
33 DDI ss1429613842 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1580216476 Apr 01, 2015 (144)
35 EVA_DECODE ss1588740491 Apr 01, 2015 (144)
36 EVA_SVP ss1712618953 Apr 01, 2015 (144)
37 HAMMER_LAB ss1800155305 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1922475058 Feb 12, 2016 (147)
39 GENOMED ss1969542406 Jul 19, 2016 (147)
40 JJLAB ss2021807662 Sep 14, 2016 (149)
41 USC_VALOUEV ss2149904106 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2256559440 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2625405715 Nov 08, 2017 (151)
44 GRF ss2705317135 Nov 08, 2017 (151)
45 GNOMAD ss2800143085 Nov 08, 2017 (151)
46 SWEGEN ss2993338404 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3024671362 Nov 08, 2017 (151)
48 CSHL ss3345306180 Nov 08, 2017 (151)
49 ILLUMINA ss3638447044 Oct 12, 2018 (152)
50 ILLUMINA ss3643401582 Oct 12, 2018 (152)
51 URBANLAB ss3647545440 Oct 12, 2018 (152)
52 EGCUT_WGS ss3661263868 Jul 13, 2019 (153)
53 EVA_DECODE ss3710459927 Jul 13, 2019 (153)
54 ACPOP ss3730425332 Jul 13, 2019 (153)
55 EVA ss3760802240 Jul 13, 2019 (153)
56 PACBIO ss3784487246 Jul 13, 2019 (153)
57 PACBIO ss3789977088 Jul 13, 2019 (153)
58 PACBIO ss3794851662 Jul 13, 2019 (153)
59 KHV_HUMAN_GENOMES ss3803934145 Jul 13, 2019 (153)
60 EVA ss3828117894 Apr 25, 2020 (154)
61 EVA ss3837491888 Apr 25, 2020 (154)
62 EVA ss3842923041 Apr 25, 2020 (154)
63 SGDP_PRJ ss3857154625 Apr 25, 2020 (154)
64 KRGDB ss3903190851 Apr 25, 2020 (154)
65 KOGIC ss3952587722 Apr 25, 2020 (154)
66 EVA ss4017110532 Apr 27, 2021 (155)
67 TOPMED ss4586714221 Apr 27, 2021 (155)
68 TOMMO_GENOMICS ss5161985210 Apr 27, 2021 (155)
69 1000G_HIGH_COVERAGE ss5256334863 Oct 12, 2022 (156)
70 EVA ss5343837799 Oct 12, 2022 (156)
71 HUGCELL_USP ss5455442144 Oct 12, 2022 (156)
72 EVA ss5507233722 Oct 12, 2022 (156)
73 1000G_HIGH_COVERAGE ss5535933158 Oct 12, 2022 (156)
74 SANFORD_IMAGENETICS ss5633363224 Oct 12, 2022 (156)
75 TOMMO_GENOMICS ss5694981356 Oct 12, 2022 (156)
76 YY_MCH ss5804322643 Oct 12, 2022 (156)
77 EVA ss5826597714 Oct 12, 2022 (156)
78 EVA ss5853874404 Oct 12, 2022 (156)
79 EVA ss5871358350 Oct 12, 2022 (156)
80 EVA ss5961721537 Oct 12, 2022 (156)
81 1000Genomes NC_000003.11 - 143688761 Oct 12, 2018 (152)
82 1000Genomes_30x NC_000003.12 - 143969919 Oct 12, 2022 (156)
83 Genetic variation in the Estonian population NC_000003.11 - 143688761 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000003.11 - 143688761 Apr 25, 2020 (154)
85 gnomAD - Genomes NC_000003.12 - 143969919 Apr 27, 2021 (155)
86 Genome of the Netherlands Release 5 NC_000003.11 - 143688761 Apr 25, 2020 (154)
87 HapMap NC_000003.12 - 143969919 Apr 25, 2020 (154)
88 KOREAN population from KRGDB NC_000003.11 - 143688761 Apr 25, 2020 (154)
89 Korean Genome Project NC_000003.12 - 143969919 Apr 25, 2020 (154)
90 Northern Sweden NC_000003.11 - 143688761 Jul 13, 2019 (153)
91 Qatari NC_000003.11 - 143688761 Apr 25, 2020 (154)
92 SGDP_PRJ NC_000003.11 - 143688761 Apr 25, 2020 (154)
93 Siberian NC_000003.11 - 143688761 Apr 25, 2020 (154)
94 8.3KJPN NC_000003.11 - 143688761 Apr 27, 2021 (155)
95 14KJPN NC_000003.12 - 143969919 Oct 12, 2022 (156)
96 TopMed NC_000003.12 - 143969919 Apr 27, 2021 (155)
97 A Vietnamese Genetic Variation Database NC_000003.11 - 143688761 Jul 13, 2019 (153)
98 ALFA NC_000003.12 - 143969919 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10368245, ss3903190851 NC_000003.11:143688760:C:A NC_000003.12:143969918:C:A (self)
10368245, ss3903190851 NC_000003.11:143688760:C:G NC_000003.12:143969918:C:G (self)
ss79081322 NC_000003.9:145171458:C:T NC_000003.12:143969918:C:T (self)
ss92309487, ss111056143, ss112536284, ss117304678, ss162683246, ss164481359, ss167280358, ss203291697, ss277382996, ss1588740491, ss1712618953, ss3643401582 NC_000003.10:145171450:C:T NC_000003.12:143969918:C:T (self)
17788402, 7002116, 6381415, 4350813, 10368245, 3710197, 4516988, 9171605, 2420460, 19954517, 2159795, ss220473282, ss232065356, ss239430166, ss650726859, ss979251374, ss1070897980, ss1306512927, ss1429613842, ss1580216476, ss1800155305, ss1922475058, ss1969542406, ss2021807662, ss2149904106, ss2625405715, ss2705317135, ss2800143085, ss2993338404, ss3345306180, ss3638447044, ss3661263868, ss3730425332, ss3760802240, ss3784487246, ss3789977088, ss3794851662, ss3828117894, ss3837491888, ss3857154625, ss3903190851, ss4017110532, ss5161985210, ss5343837799, ss5507233722, ss5633363224, ss5826597714, ss5961721537 NC_000003.11:143688760:C:T NC_000003.12:143969918:C:T (self)
23459093, 126384288, 2474391, 8965723, 28818460, 424091776, 12547095692, ss2256559440, ss3024671362, ss3647545440, ss3710459927, ss3803934145, ss3842923041, ss3952587722, ss4586714221, ss5256334863, ss5455442144, ss5535933158, ss5694981356, ss5804322643, ss5853874404, ss5871358350 NC_000003.12:143969918:C:T NC_000003.12:143969918:C:T (self)
ss21956946 NT_005612.14:50183914:C:T NC_000003.12:143969918:C:T (self)
ss65736, ss5936333, ss44418908, ss65719615, ss74855114, ss96059062, ss106303337, ss119364680, ss120245563, ss133143558, ss139201823, ss156291975, ss174303020, ss244256423 NT_005612.16:50183906:C:T NC_000003.12:143969918: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 rs723490

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