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dbSNP Short Genetic Variations

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.

rs7914558

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr10:103016151 (GRCh38.p12) 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=0.41113 (51625/125568, TOPMED)
A=0.4177 (32870/78700, PAGE_STUDY)
A=0.4136 (12898/31182, GnomAD) (+ 6 more)
A=0.441 (2211/5008, 1000G)
A=0.489 (2192/4480, Estonian)
A=0.388 (1495/3854, ALSPAC)
A=0.385 (1428/3708, TWINSUK)
A=0.35 (212/600, NorthernSweden)
G=0.40 (84/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CNNM2 : Intron Variant
Publications
12 citations
Genomic View
See rs on genome
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.p12 chr 10 NC_000010.11:g.103016151G>A
GRCh37.p13 chr 10 NC_000010.10:g.104775908G>A
CNNM2 RefSeqGene NG_031932.1:g.102834G>A
Gene: CNNM2, cyclin and CBS domain divalent metal cation transport mediator 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CNNM2 transcript variant 1 NM_017649.5:c. N/A Intron Variant
CNNM2 transcript variant 2 NM_199076.3:c. N/A Intron Variant
CNNM2 transcript variant 3 NM_199077.2:c. N/A Genic Downstream Transcript Variant
CNNM2 transcript variant X4 XM_005269933.4:c. N/A Genic Downstream Transcript Variant
CNNM2 transcript variant X6 XM_006717908.2:c. N/A Genic Downstream Transcript Variant
CNNM2 transcript variant X5 XM_011539911.3:c. N/A Genic Downstream Transcript Variant
CNNM2 transcript variant X1 XR_001747118.1:n. N/A Intron Variant
CNNM2 transcript variant X2 XR_001747119.2:n. N/A Intron Variant
CNNM2 transcript variant X7 XR_001747121.1:n. N/A Intron Variant
CNNM2 transcript variant X8 XR_945782.3:n. N/A Intron Variant
CNNM2 transcript variant X3 XR_001747120.1:n. N/A Genic Downstream 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
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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 125568 G=0.58887 A=0.41113
The PAGE Study Global Study-wide 78700 G=0.5823 A=0.4177
The PAGE Study AfricanAmerican Sub 32516 G=0.6261 A=0.3739
The PAGE Study Mexican Sub 10810 G=0.5761 A=0.4239
The PAGE Study Asian Sub 8318 G=0.525 A=0.475
The PAGE Study PuertoRican Sub 7918 G=0.571 A=0.429
The PAGE Study NativeHawaiian Sub 4534 G=0.416 A=0.584
The PAGE Study Cuban Sub 4228 G=0.567 A=0.433
The PAGE Study Dominican Sub 3828 G=0.578 A=0.422
The PAGE Study CentralAmerican Sub 2450 G=0.598 A=0.402
The PAGE Study SouthAmerican Sub 1982 G=0.592 A=0.408
The PAGE Study NativeAmerican Sub 1260 G=0.594 A=0.406
The PAGE Study SouthAsian Sub 856 G=0.55 A=0.45
gnomAD - Genomes Global Study-wide 31182 G=0.5864 A=0.4136
gnomAD - Genomes European Sub 18788 G=0.5810 A=0.4190
gnomAD - Genomes African Sub 8646 G=0.633 A=0.367
gnomAD - Genomes East Asian Sub 1534 G=0.398 A=0.602
gnomAD - Genomes Other Sub 1080 G=0.587 A=0.413
gnomAD - Genomes American Sub 844 G=0.59 A=0.41
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.53 A=0.47
1000Genomes Global Study-wide 5008 G=0.559 A=0.441
1000Genomes African Sub 1322 G=0.666 A=0.334
1000Genomes East Asian Sub 1008 G=0.415 A=0.585
1000Genomes Europe Sub 1006 G=0.583 A=0.417
1000Genomes South Asian Sub 978 G=0.52 A=0.48
1000Genomes American Sub 694 G=0.58 A=0.42
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.511 A=0.489
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.612 A=0.388
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.615 A=0.385
Northern Sweden ACPOP Study-wide 600 G=0.65 A=0.35
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.40 A=0.60
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 G= A Note
GRCh38.p12 chr 10 NC_000010.11:g.103016151= NC_000010.11:g.10301615...

NC_000010.11:g.103016151G>A

GRCh37.p13 chr 10 NC_000010.10:g.104775908= NC_000010.10:g.10477590...

NC_000010.10:g.104775908G>A

CNNM2 RefSeqGene NG_031932.1:g.102834= NG_031932.1:g.102834G>A
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#.

85 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss12099579 Jul 11, 2003 (116)
2 SC_SNP ss16075979 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19183667 Feb 27, 2004 (120)
4 SSAHASNP ss20645552 Apr 05, 2004 (121)
5 ILLUMINA ss75221474 Dec 06, 2007 (129)
6 HUMANGENOME_JCVI ss97580666 Feb 05, 2009 (130)
7 BGI ss102907572 Dec 01, 2009 (131)
8 1000GENOMES ss109707528 Jan 24, 2009 (130)
9 KRIBB_YJKIM ss119574960 Dec 01, 2009 (131)
10 ENSEMBL ss138831550 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss168719874 Jul 04, 2010 (132)
12 ILLUMINA ss174616051 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss174728735 Jul 04, 2010 (132)
14 BUSHMAN ss201948504 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss207401773 Jul 04, 2010 (132)
16 1000GENOMES ss211032770 Jul 14, 2010 (132)
17 1000GENOMES ss224909638 Jul 14, 2010 (132)
18 1000GENOMES ss235312176 Jul 15, 2010 (132)
19 1000GENOMES ss241991640 Jul 15, 2010 (132)
20 BL ss254582051 May 09, 2011 (134)
21 GMI ss280752084 May 04, 2012 (137)
22 PJP ss290920261 May 09, 2011 (134)
23 ILLUMINA ss410778588 Sep 17, 2011 (135)
24 EXOME_CHIP ss491440057 May 04, 2012 (137)
25 ILLUMINA ss537530378 Sep 08, 2015 (146)
26 SSMP ss657261208 Apr 25, 2013 (138)
27 ILLUMINA ss780686890 Sep 08, 2015 (146)
28 ILLUMINA ss783360430 Sep 08, 2015 (146)
29 EVA-GONL ss987861765 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1077253537 Aug 21, 2014 (142)
31 1000GENOMES ss1338841181 Aug 21, 2014 (142)
32 DDI ss1426427687 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1575325423 Apr 01, 2015 (144)
34 EVA_DECODE ss1597536781 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1625312832 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1668306865 Apr 01, 2015 (144)
37 EVA_SVP ss1713206959 Apr 01, 2015 (144)
38 ILLUMINA ss1751943998 Sep 08, 2015 (146)
39 HAMMER_LAB ss1806543807 Sep 08, 2015 (146)
40 ILLUMINA ss1917851126 Feb 12, 2016 (147)
41 WEILL_CORNELL_DGM ss1931224959 Feb 12, 2016 (147)
42 ILLUMINA ss1946291986 Feb 12, 2016 (147)
43 ILLUMINA ss1959290510 Feb 12, 2016 (147)
44 GENOMED ss1967211369 Jul 19, 2016 (147)
45 JJLAB ss2026342954 Sep 14, 2016 (149)
46 ILLUMINA ss2094789059 Dec 20, 2016 (150)
47 ILLUMINA ss2095017053 Dec 20, 2016 (150)
48 USC_VALOUEV ss2154621834 Nov 08, 2017 (151)
49 HUMAN_LONGEVITY ss2177606488 Dec 20, 2016 (150)
50 TOPMED ss2340728738 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2627639588 Nov 08, 2017 (151)
52 ILLUMINA ss2632755429 Nov 08, 2017 (151)
53 GRF ss2698875618 Nov 08, 2017 (151)
54 GNOMAD ss2892769237 Nov 08, 2017 (151)
55 AFFY ss2984922268 Nov 08, 2017 (151)
56 AFFY ss2985569541 Nov 08, 2017 (151)
57 SWEGEN ss3007058737 Nov 08, 2017 (151)
58 ILLUMINA ss3021270619 Nov 08, 2017 (151)
59 BIOINF_KMB_FNS_UNIBA ss3026961199 Nov 08, 2017 (151)
60 TOPMED ss3128998944 Nov 08, 2017 (151)
61 CSHL ss3349285601 Nov 08, 2017 (151)
62 ILLUMINA ss3626522662 Oct 12, 2018 (152)
63 ILLUMINA ss3626522663 Oct 12, 2018 (152)
64 ILLUMINA ss3634421419 Oct 12, 2018 (152)
65 ILLUMINA ss3637871056 Oct 12, 2018 (152)
66 ILLUMINA ss3640128760 Oct 12, 2018 (152)
67 ILLUMINA ss3642872758 Oct 12, 2018 (152)
68 ILLUMINA ss3644544733 Oct 12, 2018 (152)
69 URBANLAB ss3649453787 Oct 12, 2018 (152)
70 ILLUMINA ss3651629625 Oct 12, 2018 (152)
71 ILLUMINA ss3651629626 Oct 12, 2018 (152)
72 ILLUMINA ss3653693135 Oct 12, 2018 (152)
73 EGCUT_WGS ss3674469685 Jul 13, 2019 (153)
74 EVA_DECODE ss3690574147 Jul 13, 2019 (153)
75 ILLUMINA ss3725184656 Jul 13, 2019 (153)
76 ACPOP ss3737632553 Jul 13, 2019 (153)
77 ILLUMINA ss3744371339 Jul 13, 2019 (153)
78 ILLUMINA ss3744722366 Jul 13, 2019 (153)
79 EVA ss3748534771 Jul 13, 2019 (153)
80 PAGE_CC ss3771579986 Jul 13, 2019 (153)
81 ILLUMINA ss3772222687 Jul 13, 2019 (153)
82 PACBIO ss3786772460 Jul 13, 2019 (153)
83 PACBIO ss3791936957 Jul 13, 2019 (153)
84 PACBIO ss3796819059 Jul 13, 2019 (153)
85 KHV_HUMAN_GENOMES ss3813896628 Jul 13, 2019 (153)
86 1000Genomes NC_000010.10 - 104775908 Oct 12, 2018 (152)
87 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 104775908 Oct 12, 2018 (152)
88 Genetic variation in the Estonian population NC_000010.10 - 104775908 Oct 12, 2018 (152)
89 gnomAD - Genomes NC_000010.10 - 104775908 Jul 13, 2019 (153)
90 Northern Sweden NC_000010.10 - 104775908 Jul 13, 2019 (153)
91 The PAGE Study NC_000010.11 - 103016151 Jul 13, 2019 (153)
92 TopMed NC_000010.11 - 103016151 Oct 12, 2018 (152)
93 UK 10K study - Twins NC_000010.10 - 104775908 Oct 12, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000010.10 - 104775908 Jul 13, 2019 (153)
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
ss109707528, ss168719874, ss174728735, ss201948504, ss207401773, ss211032770, ss254582051, ss280752084, ss290920261, ss1597536781, ss1713206959, ss3642872758 NC_000010.9:104765897:G:A NC_000010.11:103016150:G:A (self)
51280498, 28474753, 20207933, 140116812, 10917418, 28474753, 6320685, ss224909638, ss235312176, ss241991640, ss491440057, ss537530378, ss657261208, ss780686890, ss783360430, ss987861765, ss1077253537, ss1338841181, ss1426427687, ss1575325423, ss1625312832, ss1668306865, ss1751943998, ss1806543807, ss1917851126, ss1931224959, ss1946291986, ss1959290510, ss1967211369, ss2026342954, ss2094789059, ss2095017053, ss2154621834, ss2340728738, ss2627639588, ss2632755429, ss2698875618, ss2892769237, ss2984922268, ss2985569541, ss3007058737, ss3021270619, ss3349285601, ss3626522662, ss3626522663, ss3634421419, ss3637871056, ss3640128760, ss3644544733, ss3651629625, ss3651629626, ss3653693135, ss3674469685, ss3737632553, ss3744371339, ss3744722366, ss3748534771, ss3772222687, ss3786772460, ss3791936957, ss3796819059 NC_000010.10:104775907:G:A NC_000010.11:103016150:G:A (self)
801455, 50371107, ss2177606488, ss3026961199, ss3128998944, ss3649453787, ss3690574147, ss3725184656, ss3771579986, ss3813896628 NC_000010.11:103016150:G:A NC_000010.11:103016150:G:A (self)
ss12099579 NT_030059.10:23214465:G:A NC_000010.11:103016150:G:A (self)
ss16075979, ss19183667, ss20645552 NT_030059.11:23524433:G:A NC_000010.11:103016150:G:A (self)
ss75221474, ss97580666, ss102907572, ss119574960, ss138831550, ss174616051, ss410778588 NT_030059.13:55580371:G:A NC_000010.11:103016150:G:A (self)
Help

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

12 citations for rs7914558
PMID Title Author Year Journal
21926974 Genome-wide association study identifies five new schizophrenia loci. Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium. et al. 2011 Nature genetics
22078159 Two patients walk into a clinic...a genomics perspective on the future of schizophrenia. Corvin AP et al. 2011 BMC biology
22520855 Association study of a new schizophrenia susceptibility locus of 10q24.32-33 in a Han Chinese population. Guan F et al. 2012 Schizophrenia research
23507081 Using genetic, cognitive and multi-modal neuroimaging data to identify ultra-high-risk and first-episode psychosis at the individual level. Pettersson-Yeo W et al. 2013 Psychological medicine
23776546 Meta-analysis indicates that the European GWAS-identified risk SNP rs1344706 within ZNF804A is not associated with schizophrenia in Han Chinese population. Li M et al. 2013 PloS one
23871474 A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation. Psychosis Endophenotypes International Consortium. et al. 2014 Biological psychiatry
24174267 A population-based study of genetic variation and psychotic experiences in adolescents. Zammit S et al. 2014 Schizophrenia bulletin
24311551 Effects of a novel schizophrenia risk variant rs7914558 at CNNM2 on brain structure and attributional style. Rose EJ et al. 2014 The British journal of psychiatry
24339136 Neurophysiologic effect of GWAS derived schizophrenia and bipolar risk variants. Hall MH et al. 2014 American journal of medical genetics. Part B, Neuropsychiatric genetics
27028512 Genetic Evaluation of Schizophrenia Using the Illumina HumanExome Chip. Moons T et al. 2016 PloS one
27481827 Testing the Validity of Taxonic Schizotypy Using Genetic and Environmental Risk Variables. Morton SE et al. 2017 Schizophrenia bulletin
28277567 Evidence of AS3MT<sup>d2d3</sup>-Associated Variants within 10q24.32-33 in the Genetic Risk of Major Affective Disorders. Li L et al. 2017 Molecular neuropsychiatry

Genomic regions, transcripts, and products
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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.post246+3cda961