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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.

rs12021500

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:113524369 (GRCh38.p13) 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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.244735 (64779/264690, TOPMED)
C=0.238799 (33353/139670, GnomAD)
C=0.24076 (4548/18890, ALFA) (+ 14 more)
T=0.46217 (7746/16760, 8.3KJPN)
C=0.2873 (1439/5008, 1000G)
C=0.2737 (1226/4480, Estonian)
C=0.2307 (889/3854, ALSPAC)
C=0.2346 (870/3708, TWINSUK)
T=0.3587 (1051/2930, KOREAN)
T=0.3483 (638/1832, Korea1K)
C=0.235 (235/998, GoNL)
C=0.257 (154/600, NorthernSweden)
T=0.372 (96/258, SGDP_PRJ)
C=0.194 (42/216, Qatari)
T=0.421 (90/214, Vietnamese)
C=0.15 (6/40, GENOME_DK)
T=0.36 (8/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MAGI3 : Intron Variant
Publications
0 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.p13 chr 1 NC_000001.11:g.113524369T>A
GRCh38.p13 chr 1 NC_000001.11:g.113524369T>C
GRCh38.p13 chr 1 NC_000001.11:g.113524369T>G
GRCh37.p13 chr 1 NC_000001.10:g.114066991T>A
GRCh37.p13 chr 1 NC_000001.10:g.114066991T>C
GRCh37.p13 chr 1 NC_000001.10:g.114066991T>G
Gene: MAGI3, membrane associated guanylate kinase, WW and PDZ domain containing 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MAGI3 transcript variant 1 NM_001142782.2:c.317-2514…

NM_001142782.2:c.317-25146T>A

N/A Intron Variant
MAGI3 transcript variant 2 NM_152900.3:c.317-25146T>A N/A Intron Variant
MAGI3 transcript variant X3 XM_005270737.3:c.317-2514…

XM_005270737.3:c.317-25146T>A

N/A Intron Variant
MAGI3 transcript variant X1 XM_011541208.2:c.-1940-25…

XM_011541208.2:c.-1940-25146T>A

N/A Intron Variant
MAGI3 transcript variant X2 XM_017000974.1:c.317-2514…

XM_017000974.1:c.317-25146T>A

N/A Intron Variant
MAGI3 transcript variant X6 XM_017000975.1:c. N/A Genic Upstream Transcript Variant
MAGI3 transcript variant X5 XR_001737106.1:n. N/A Intron Variant
MAGI3 transcript variant X4 XR_946601.2:n. 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 T=0.75924 C=0.24076
European Sub 14286 T=0.75493 C=0.24507
African Sub 2946 T=0.8136 C=0.1864
African Others Sub 114 T=0.868 C=0.132
African American Sub 2832 T=0.8114 C=0.1886
Asian Sub 112 T=0.411 C=0.589
East Asian Sub 86 T=0.33 C=0.67
Other Asian Sub 26 T=0.69 C=0.31
Latin American 1 Sub 146 T=0.740 C=0.260
Latin American 2 Sub 610 T=0.633 C=0.367
South Asian Sub 98 T=0.89 C=0.11
Other Sub 692 T=0.770 C=0.230


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 T=0.755265 C=0.244735
gnomAD - Genomes Global Study-wide 139670 T=0.761201 C=0.238799
gnomAD - Genomes European Sub 75716 T=0.75560 C=0.24440
gnomAD - Genomes African Sub 41784 T=0.81368 C=0.18632
gnomAD - Genomes American Sub 13604 T=0.72457 C=0.27543
gnomAD - Genomes Ashkenazi Jewish Sub 3314 T=0.7677 C=0.2323
gnomAD - Genomes East Asian Sub 3114 T=0.3523 C=0.6477
gnomAD - Genomes Other Sub 2138 T=0.7526 C=0.2474
8.3KJPN JAPANESE Study-wide 16760 T=0.46217 C=0.53783
1000Genomes Global Study-wide 5008 T=0.7127 C=0.2873
1000Genomes African Sub 1322 T=0.8555 C=0.1445
1000Genomes East Asian Sub 1008 T=0.3909 C=0.6091
1000Genomes Europe Sub 1006 T=0.7644 C=0.2356
1000Genomes South Asian Sub 978 T=0.830 C=0.170
1000Genomes American Sub 694 T=0.667 C=0.333
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7263 C=0.2737
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7693 C=0.2307
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7654 C=0.2346
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3587 A=0.0000, C=0.6413, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.3483 C=0.6517
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.765 C=0.235
Northern Sweden ACPOP Study-wide 600 T=0.743 C=0.257
SGDP_PRJ Global Study-wide 258 T=0.372 C=0.628
Qatari Global Study-wide 216 T=0.806 C=0.194
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.421 C=0.579
The Danish reference pan genome Danish Study-wide 40 T=0.85 C=0.15
Siberian Global Study-wide 22 T=0.36 C=0.64
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 T= A C G
GRCh38.p13 chr 1 NC_000001.11:g.113524369= NC_000001.11:g.113524369T>A NC_000001.11:g.113524369T>C NC_000001.11:g.113524369T>G
GRCh37.p13 chr 1 NC_000001.10:g.114066991= NC_000001.10:g.114066991T>A NC_000001.10:g.114066991T>C NC_000001.10:g.114066991T>G
MAGI3 transcript variant 1 NM_001142782.1:c.317-25146= NM_001142782.1:c.317-25146T>A NM_001142782.1:c.317-25146T>C NM_001142782.1:c.317-25146T>G
MAGI3 transcript variant 1 NM_001142782.2:c.317-25146= NM_001142782.2:c.317-25146T>A NM_001142782.2:c.317-25146T>C NM_001142782.2:c.317-25146T>G
MAGI3 transcript variant 2 NM_152900.2:c.317-25146= NM_152900.2:c.317-25146T>A NM_152900.2:c.317-25146T>C NM_152900.2:c.317-25146T>G
MAGI3 transcript variant 2 NM_152900.3:c.317-25146= NM_152900.3:c.317-25146T>A NM_152900.3:c.317-25146T>C NM_152900.3:c.317-25146T>G
MAGI3 transcript variant X1 XM_005270736.1:c.317-25146= XM_005270736.1:c.317-25146T>A XM_005270736.1:c.317-25146T>C XM_005270736.1:c.317-25146T>G
MAGI3 transcript variant X2 XM_005270737.1:c.317-25146= XM_005270737.1:c.317-25146T>A XM_005270737.1:c.317-25146T>C XM_005270737.1:c.317-25146T>G
MAGI3 transcript variant X3 XM_005270737.3:c.317-25146= XM_005270737.3:c.317-25146T>A XM_005270737.3:c.317-25146T>C XM_005270737.3:c.317-25146T>G
MAGI3 transcript variant X1 XM_011541208.2:c.-1940-25146= XM_011541208.2:c.-1940-25146T>A XM_011541208.2:c.-1940-25146T>C XM_011541208.2:c.-1940-25146T>G
MAGI3 transcript variant X2 XM_017000974.1:c.317-25146= XM_017000974.1:c.317-25146T>A XM_017000974.1:c.317-25146T>C XM_017000974.1:c.317-25146T>G
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#.

51 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069701 Feb 28, 2004 (120)
2 1000GENOMES ss108536659 Jan 23, 2009 (130)
3 COMPLETE_GENOMICS ss165056795 Jul 04, 2010 (132)
4 COMPLETE_GENOMICS ss167017590 Jul 04, 2010 (132)
5 BUSHMAN ss198953760 Jul 04, 2010 (132)
6 1000GENOMES ss218605793 Jul 14, 2010 (132)
7 1000GENOMES ss230698200 Jul 14, 2010 (132)
8 1000GENOMES ss238354607 Jul 15, 2010 (132)
9 BL ss253396225 May 09, 2011 (134)
10 GMI ss275984231 May 04, 2012 (137)
11 GMI ss284124090 Apr 25, 2013 (138)
12 TISHKOFF ss554593849 Apr 25, 2013 (138)
13 SSMP ss648323194 Apr 25, 2013 (138)
14 EVA-GONL ss975586727 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1068205078 Aug 21, 2014 (142)
16 1000GENOMES ss1292495158 Aug 21, 2014 (142)
17 DDI ss1425942102 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1574333497 Apr 01, 2015 (144)
19 EVA_DECODE ss1584967572 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1601023722 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1644017755 Apr 01, 2015 (144)
22 HAMMER_LAB ss1794956518 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1918787047 Feb 12, 2016 (147)
24 GENOMED ss1966845206 Jul 19, 2016 (147)
25 JJLAB ss2019917959 Sep 14, 2016 (149)
26 USC_VALOUEV ss2147936668 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2165842494 Dec 20, 2016 (150)
28 TOPMED ss2328206884 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2624468612 Nov 08, 2017 (151)
30 GRF ss2697866989 Nov 08, 2017 (151)
31 GNOMAD ss2759738793 Nov 08, 2017 (151)
32 SWEGEN ss2987464374 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3023723482 Nov 08, 2017 (151)
34 TOPMED ss3087217068 Nov 08, 2017 (151)
35 CSHL ss3343642459 Nov 08, 2017 (151)
36 EGCUT_WGS ss3655553333 Jul 12, 2019 (153)
37 EVA_DECODE ss3687562032 Jul 12, 2019 (153)
38 ACPOP ss3727402285 Jul 12, 2019 (153)
39 EVA ss3746691566 Jul 12, 2019 (153)
40 PACBIO ss3783524263 Jul 12, 2019 (153)
41 PACBIO ss3789165404 Jul 12, 2019 (153)
42 PACBIO ss3794038339 Jul 12, 2019 (153)
43 KHV_HUMAN_GENOMES ss3799694394 Jul 12, 2019 (153)
44 EVA ss3826378215 Apr 25, 2020 (154)
45 EVA ss3836580808 Apr 25, 2020 (154)
46 EVA ss3841989245 Apr 25, 2020 (154)
47 SGDP_PRJ ss3849682684 Apr 25, 2020 (154)
48 KRGDB ss3894780573 Apr 25, 2020 (154)
49 KOGIC ss3945279498 Apr 25, 2020 (154)
50 TOPMED ss4464154946 Apr 25, 2021 (155)
51 TOMMO_GENOMICS ss5145752337 Apr 25, 2021 (155)
52 1000Genomes NC_000001.10 - 114066991 Oct 11, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 114066991 Oct 11, 2018 (152)
54 Genetic variation in the Estonian population NC_000001.10 - 114066991 Oct 11, 2018 (152)
55 The Danish reference pan genome NC_000001.10 - 114066991 Apr 25, 2020 (154)
56 gnomAD - Genomes NC_000001.11 - 113524369 Apr 25, 2021 (155)
57 Genome of the Netherlands Release 5 NC_000001.10 - 114066991 Apr 25, 2020 (154)
58 KOREAN population from KRGDB NC_000001.10 - 114066991 Apr 25, 2020 (154)
59 Korean Genome Project NC_000001.11 - 113524369 Apr 25, 2020 (154)
60 Northern Sweden NC_000001.10 - 114066991 Jul 12, 2019 (153)
61 Qatari NC_000001.10 - 114066991 Apr 25, 2020 (154)
62 SGDP_PRJ NC_000001.10 - 114066991 Apr 25, 2020 (154)
63 Siberian NC_000001.10 - 114066991 Apr 25, 2020 (154)
64 8.3KJPN NC_000001.10 - 114066991 Apr 25, 2021 (155)
65 TopMed NC_000001.11 - 113524369 Apr 25, 2021 (155)
66 UK 10K study - Twins NC_000001.10 - 114066991 Oct 11, 2018 (152)
67 A Vietnamese Genetic Variation Database NC_000001.10 - 114066991 Jul 12, 2019 (153)
68 ALFA NC_000001.11 - 113524369 Apr 25, 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
1957967, ss3894780573 NC_000001.10:114066990:T:A NC_000001.11:113524368:T:A (self)
ss108536659, ss165056795, ss167017590, ss198953760, ss253396225, ss275984231, ss284124090, ss1584967572 NC_000001.9:113868513:T:C NC_000001.11:113524368:T:C (self)
3273270, 1810945, 1291581, 1671296, 787599, 1957967, 687150, 828977, 1699664, 453022, 3721644, 1810945, 392120, ss218605793, ss230698200, ss238354607, ss554593849, ss648323194, ss975586727, ss1068205078, ss1292495158, ss1425942102, ss1574333497, ss1601023722, ss1644017755, ss1794956518, ss1918787047, ss1966845206, ss2019917959, ss2147936668, ss2328206884, ss2624468612, ss2697866989, ss2759738793, ss2987464374, ss3343642459, ss3655553333, ss3727402285, ss3746691566, ss3783524263, ss3789165404, ss3794038339, ss3826378215, ss3836580808, ss3849682684, ss3894780573, ss5145752337 NC_000001.10:114066990:T:C NC_000001.11:113524368:T:C (self)
23149260, 1657499, 17488090, 27761281, 8847630834, ss2165842494, ss3023723482, ss3087217068, ss3687562032, ss3799694394, ss3841989245, ss3945279498, ss4464154946 NC_000001.11:113524368:T:C NC_000001.11:113524368:T:C (self)
ss18069701 NT_019273.16:5062938:T:C NC_000001.11:113524368:T:C (self)
1957967, ss3894780573 NC_000001.10:114066990:T:G NC_000001.11:113524368:T:G (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 rs12021500

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.post596+ae089ad