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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.

rs12021513

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:113574267 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.302988 (80198/264690, TOPMED)
T=0.294288 (41168/139890, GnomAD)
T=0.30418 (5746/18890, ALFA) (+ 14 more)
C=0.42840 (7180/16760, 8.3KJPN)
T=0.3468 (1737/5008, 1000G)
T=0.3455 (1548/4480, Estonian)
T=0.3137 (1209/3854, ALSPAC)
T=0.3039 (1127/3708, TWINSUK)
C=0.3498 (1025/2930, KOREAN)
C=0.3439 (630/1832, Korea1K)
T=0.303 (302/998, GoNL)
T=0.288 (173/600, NorthernSweden)
C=0.363 (109/300, SGDP_PRJ)
T=0.324 (70/216, Qatari)
C=0.416 (89/214, Vietnamese)
T=0.25 (10/40, GENOME_DK)
C=0.43 (12/28, 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.113574267C>A
GRCh38.p13 chr 1 NC_000001.11:g.113574267C>G
GRCh38.p13 chr 1 NC_000001.11:g.113574267C>T
GRCh37.p13 chr 1 NC_000001.10:g.114116889C>A
GRCh37.p13 chr 1 NC_000001.10:g.114116889C>G
GRCh37.p13 chr 1 NC_000001.10:g.114116889C>T
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.434-6275…

NM_001142782.2:c.434-6275C>A

N/A Intron Variant
MAGI3 transcript variant 2 NM_152900.3:c.434-6275C>A N/A Intron Variant
MAGI3 transcript variant X3 XM_005270737.3:c.434-6275…

XM_005270737.3:c.434-6275C>A

N/A Intron Variant
MAGI3 transcript variant X1 XM_011541208.2:c.-1823-62…

XM_011541208.2:c.-1823-6275C>A

N/A Intron Variant
MAGI3 transcript variant X2 XM_017000974.1:c.434-6275…

XM_017000974.1:c.434-6275C>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 C=0.69582 T=0.30418
European Sub 14286 C=0.67990 T=0.32010
African Sub 2946 C=0.8174 T=0.1826
African Others Sub 114 C=0.877 T=0.123
African American Sub 2832 C=0.8150 T=0.1850
Asian Sub 112 C=0.429 T=0.571
East Asian Sub 86 C=0.35 T=0.65
Other Asian Sub 26 C=0.69 T=0.31
Latin American 1 Sub 146 C=0.685 T=0.315
Latin American 2 Sub 610 C=0.508 T=0.492
South Asian Sub 98 C=0.78 T=0.22
Other Sub 692 C=0.707 T=0.293


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=0.697012 T=0.302988
gnomAD - Genomes Global Study-wide 139890 C=0.705712 T=0.294288
gnomAD - Genomes European Sub 75786 C=0.68183 T=0.31817
gnomAD - Genomes African Sub 41888 C=0.81264 T=0.18736
gnomAD - Genomes American Sub 13620 C=0.59163 T=0.40837
gnomAD - Genomes Ashkenazi Jewish Sub 3316 C=0.7204 T=0.2796
gnomAD - Genomes East Asian Sub 3126 C=0.3420 T=0.6580
gnomAD - Genomes Other Sub 2154 C=0.6931 T=0.3069
8.3KJPN JAPANESE Study-wide 16760 C=0.42840 T=0.57160
1000Genomes Global Study-wide 5008 C=0.6532 T=0.3468
1000Genomes African Sub 1322 C=0.8419 T=0.1581
1000Genomes East Asian Sub 1008 C=0.3552 T=0.6448
1000Genomes Europe Sub 1006 C=0.6909 T=0.3091
1000Genomes South Asian Sub 978 C=0.744 T=0.256
1000Genomes American Sub 694 C=0.543 T=0.457
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6545 T=0.3455
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6863 T=0.3137
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6961 T=0.3039
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.3498 A=0.0000, G=0.0000, T=0.6502
Korean Genome Project KOREAN Study-wide 1832 C=0.3439 T=0.6561
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.697 T=0.303
Northern Sweden ACPOP Study-wide 600 C=0.712 T=0.288
SGDP_PRJ Global Study-wide 300 C=0.363 T=0.637
Qatari Global Study-wide 216 C=0.676 T=0.324
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.416 T=0.584
The Danish reference pan genome Danish Study-wide 40 C=0.75 T=0.25
Siberian Global Study-wide 28 C=0.43 T=0.57
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.p13 chr 1 NC_000001.11:g.113574267= NC_000001.11:g.113574267C>A NC_000001.11:g.113574267C>G NC_000001.11:g.113574267C>T
GRCh37.p13 chr 1 NC_000001.10:g.114116889= NC_000001.10:g.114116889C>A NC_000001.10:g.114116889C>G NC_000001.10:g.114116889C>T
MAGI3 transcript variant 1 NM_001142782.1:c.434-6275= NM_001142782.1:c.434-6275C>A NM_001142782.1:c.434-6275C>G NM_001142782.1:c.434-6275C>T
MAGI3 transcript variant 1 NM_001142782.2:c.434-6275= NM_001142782.2:c.434-6275C>A NM_001142782.2:c.434-6275C>G NM_001142782.2:c.434-6275C>T
MAGI3 transcript variant 2 NM_152900.2:c.434-6275= NM_152900.2:c.434-6275C>A NM_152900.2:c.434-6275C>G NM_152900.2:c.434-6275C>T
MAGI3 transcript variant 2 NM_152900.3:c.434-6275= NM_152900.3:c.434-6275C>A NM_152900.3:c.434-6275C>G NM_152900.3:c.434-6275C>T
MAGI3 transcript variant X1 XM_005270736.1:c.434-6275= XM_005270736.1:c.434-6275C>A XM_005270736.1:c.434-6275C>G XM_005270736.1:c.434-6275C>T
MAGI3 transcript variant X2 XM_005270737.1:c.434-6275= XM_005270737.1:c.434-6275C>A XM_005270737.1:c.434-6275C>G XM_005270737.1:c.434-6275C>T
MAGI3 transcript variant X3 XM_005270737.3:c.434-6275= XM_005270737.3:c.434-6275C>A XM_005270737.3:c.434-6275C>G XM_005270737.3:c.434-6275C>T
MAGI3 transcript variant X1 XM_011541208.2:c.-1823-6275= XM_011541208.2:c.-1823-6275C>A XM_011541208.2:c.-1823-6275C>G XM_011541208.2:c.-1823-6275C>T
MAGI3 transcript variant X2 XM_017000974.1:c.434-6275= XM_017000974.1:c.434-6275C>A XM_017000974.1:c.434-6275C>G XM_017000974.1:c.434-6275C>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#.

46 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069730 Feb 28, 2004 (120)
2 HGSV ss78307138 Dec 07, 2007 (129)
3 BUSHMAN ss198953963 Jul 04, 2010 (142)
4 GMI ss275984340 May 04, 2012 (137)
5 GMI ss284124147 Apr 25, 2013 (138)
6 PJP ss290602098 May 09, 2011 (134)
7 1000GENOMES ss328866953 May 09, 2011 (134)
8 TISHKOFF ss554594084 Apr 25, 2013 (138)
9 SSMP ss648323421 Apr 25, 2013 (138)
10 EVA-GONL ss975587042 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1068205315 Aug 21, 2014 (142)
12 1000GENOMES ss1292496359 Aug 21, 2014 (142)
13 DDI ss1425942221 Apr 01, 2015 (144)
14 EVA_GENOME_DK ss1574333692 Apr 01, 2015 (144)
15 EVA_DECODE ss1584967888 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1601024322 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1644018355 Apr 01, 2015 (144)
18 HAMMER_LAB ss1794956832 Sep 08, 2015 (146)
19 WEILL_CORNELL_DGM ss1918787326 Feb 12, 2016 (147)
20 JJLAB ss2019918116 Sep 14, 2016 (149)
21 USC_VALOUEV ss2147936827 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2165845134 Dec 20, 2016 (150)
23 TOPMED ss2328209522 Dec 20, 2016 (150)
24 SYSTEMSBIOZJU ss2624468685 Nov 08, 2017 (151)
25 GRF ss2697867134 Nov 08, 2017 (151)
26 GNOMAD ss2759742380 Nov 08, 2017 (151)
27 SWEGEN ss2987464848 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3023723581 Nov 08, 2017 (151)
29 TOPMED ss3087225228 Nov 08, 2017 (151)
30 CSHL ss3343642608 Nov 08, 2017 (151)
31 EGCUT_WGS ss3655553818 Jul 12, 2019 (153)
32 EVA_DECODE ss3687562598 Jul 12, 2019 (153)
33 ACPOP ss3727402540 Jul 12, 2019 (153)
34 EVA ss3746691966 Jul 12, 2019 (153)
35 PACBIO ss3783524357 Jul 12, 2019 (153)
36 PACBIO ss3789165480 Jul 12, 2019 (153)
37 PACBIO ss3794038415 Jul 12, 2019 (153)
38 KHV_HUMAN_GENOMES ss3799694763 Jul 12, 2019 (153)
39 EVA ss3826378389 Apr 25, 2020 (154)
40 EVA ss3836580886 Apr 25, 2020 (154)
41 EVA ss3841989324 Apr 25, 2020 (154)
42 SGDP_PRJ ss3849683265 Apr 25, 2020 (154)
43 KRGDB ss3894781274 Apr 25, 2020 (154)
44 KOGIC ss3945280097 Apr 25, 2020 (154)
45 TOPMED ss4464166314 Apr 25, 2021 (155)
46 TOMMO_GENOMICS ss5145753699 Apr 25, 2021 (155)
47 1000Genomes NC_000001.10 - 114116889 Oct 11, 2018 (152)
48 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 114116889 Oct 11, 2018 (152)
49 Genetic variation in the Estonian population NC_000001.10 - 114116889 Oct 11, 2018 (152)
50 The Danish reference pan genome NC_000001.10 - 114116889 Apr 25, 2020 (154)
51 gnomAD - Genomes NC_000001.11 - 113574267 Apr 25, 2021 (155)
52 Genome of the Netherlands Release 5 NC_000001.10 - 114116889 Apr 25, 2020 (154)
53 KOREAN population from KRGDB NC_000001.10 - 114116889 Apr 25, 2020 (154)
54 Korean Genome Project NC_000001.11 - 113574267 Apr 25, 2020 (154)
55 Northern Sweden NC_000001.10 - 114116889 Jul 12, 2019 (153)
56 Qatari NC_000001.10 - 114116889 Apr 25, 2020 (154)
57 SGDP_PRJ NC_000001.10 - 114116889 Apr 25, 2020 (154)
58 Siberian NC_000001.10 - 114116889 Apr 25, 2020 (154)
59 8.3KJPN NC_000001.10 - 114116889 Apr 25, 2021 (155)
60 TopMed NC_000001.11 - 113574267 Apr 25, 2021 (155)
61 UK 10K study - Twins NC_000001.10 - 114116889 Oct 11, 2018 (152)
62 A Vietnamese Genetic Variation Database NC_000001.10 - 114116889 Jul 12, 2019 (153)
63 ALFA NC_000001.11 - 113574267 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).

Associated ID History Updated (Build)
rs112362527 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1958668, ss3894781274 NC_000001.10:114116888:C:A NC_000001.11:113574266:C:A (self)
1958668, ss3894781274 NC_000001.10:114116888:C:G NC_000001.11:113574266:C:G (self)
ss78307138 NC_000001.8:113828930:C:T NC_000001.11:113574266:C:T (self)
ss198953963, ss275984340, ss284124147, ss290602098, ss1584967888 NC_000001.9:113918411:C:T NC_000001.11:113574266:C:T (self)
3274523, 1811628, 1292066, 1671424, 787908, 1958668, 687405, 829256, 1700245, 453181, 3723006, 1811628, 392292, ss328866953, ss554594084, ss648323421, ss975587042, ss1068205315, ss1292496359, ss1425942221, ss1574333692, ss1601024322, ss1644018355, ss1794956832, ss1918787326, ss2019918116, ss2147936827, ss2328209522, ss2624468685, ss2697867134, ss2759742380, ss2987464848, ss3343642608, ss3655553818, ss3727402540, ss3746691966, ss3783524357, ss3789165480, ss3794038415, ss3826378389, ss3836580886, ss3849683265, ss3894781274, ss5145753699 NC_000001.10:114116888:C:T NC_000001.11:113574266:C:T (self)
23158357, 1658098, 17495286, 27772649, 10630492920, ss2165845134, ss3023723581, ss3087225228, ss3687562598, ss3799694763, ss3841989324, ss3945280097, ss4464166314 NC_000001.11:113574266:C:T NC_000001.11:113574266:C:T (self)
ss18069730 NT_019273.16:5112836:C:T NC_000001.11:113574266: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 rs12021513

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