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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.

rs183951113

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:41646537 (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
G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000023 (6/264690, TOPMED)
C=0.000029 (4/139990, GnomAD)
C=0.00326 (92/28258, 14KJPN) (+ 6 more)
C=0.00274 (46/16760, 8.3KJPN)
C=0.00000 (0/14050, ALFA)
C=0.0003 (2/6404, 1000G_30x)
C=0.0002 (1/5008, 1000G)
C=0.0034 (10/2922, KOREAN)
C=0.0049 (9/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MGA : 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 14050 G=1.00000 C=0.00000
European Sub 9690 G=1.0000 C=0.0000
African Sub 2898 G=1.0000 C=0.0000
African Others Sub 114 G=1.000 C=0.000
African American Sub 2784 G=1.0000 C=0.0000
Asian Sub 112 G=1.000 C=0.000
East Asian Sub 86 G=1.00 C=0.00
Other Asian Sub 26 G=1.00 C=0.00
Latin American 1 Sub 146 G=1.000 C=0.000
Latin American 2 Sub 610 G=1.000 C=0.000
South Asian Sub 98 G=1.00 C=0.00
Other Sub 496 G=1.000 C=0.000


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 G=0.999977 C=0.000023
gnomAD - Genomes Global Study-wide 139990 G=0.999971 C=0.000029
gnomAD - Genomes European Sub 75850 G=1.00000 C=0.00000
gnomAD - Genomes African Sub 41932 G=1.00000 C=0.00000
gnomAD - Genomes American Sub 13610 G=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3130 G=0.9990 C=0.0010
gnomAD - Genomes Other Sub 2146 G=0.9995 C=0.0005
14KJPN JAPANESE Study-wide 28258 G=0.99674 C=0.00326
8.3KJPN JAPANESE Study-wide 16760 G=0.99726 C=0.00274
Allele Frequency Aggregator Total Global 14050 G=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9997 C=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 C=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9983 C=0.0017
1000Genomes_30x American Sub 980 G=1.000 C=0.000
1000Genomes Global Study-wide 5008 G=0.9998 C=0.0002
1000Genomes African Sub 1322 G=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 C=0.0010
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=1.000 C=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9966 C=0.0034
Korean Genome Project KOREAN Study-wide 1832 G=0.9951 C=0.0049
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 15 NC_000015.10:g.41646537G>C
GRCh37.p13 chr 15 NC_000015.9:g.41938735G>C
Gene: MGA, MAX dimerization protein MGA (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MGA transcript variant 8 NM_001400246.1:c.-67-2229…

NM_001400246.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant 9 NM_001400247.1:c.-67-2229…

NM_001400247.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant 2 NM_001080541.3:c. N/A Genic Upstream Transcript Variant
MGA transcript variant 1 NM_001164273.2:c. N/A Genic Upstream Transcript Variant
MGA transcript variant 3 NM_001400225.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant 4 NM_001400242.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant 5 NM_001400243.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant 6 NM_001400244.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant 7 NM_001400245.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X2 XM_005254246.4:c.-67-2229…

XM_005254246.4:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X30 XM_006720445.5:c.-308+252…

XM_006720445.5:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X29 XM_017022029.3:c.-308+249…

XM_017022029.3:c.-308+24948G>C

N/A Intron Variant
MGA transcript variant X4 XM_047432276.1:c.-67-2229…

XM_047432276.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X7 XM_047432279.1:c.-67-2229…

XM_047432279.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X8 XM_047432280.1:c.-67-2229…

XM_047432280.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X11 XM_047432281.1:c.-67-2229…

XM_047432281.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X17 XM_047432286.1:c.-67-2229…

XM_047432286.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X19 XM_047432288.1:c.-67-2229…

XM_047432288.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X22 XM_047432291.1:c.-67-2229…

XM_047432291.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X25 XM_047432295.1:c.-67-2229…

XM_047432295.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X28 XM_047432298.1:c.-67-2229…

XM_047432298.1:c.-67-22291G>C

N/A Intron Variant
MGA transcript variant X31 XM_047432299.1:c.-308+252…

XM_047432299.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X32 XM_047432300.1:c.-308+249…

XM_047432300.1:c.-308+24948G>C

N/A Intron Variant
MGA transcript variant X33 XM_047432301.1:c.-308+252…

XM_047432301.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X34 XM_047432302.1:c.-308+249…

XM_047432302.1:c.-308+24948G>C

N/A Intron Variant
MGA transcript variant X35 XM_047432303.1:c.-308+252…

XM_047432303.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X36 XM_047432304.1:c.-308+252…

XM_047432304.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X37 XM_047432305.1:c.-308+252…

XM_047432305.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X38 XM_047432306.1:c.-308+252…

XM_047432306.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X39 XM_047432307.1:c.-308+252…

XM_047432307.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X40 XM_047432308.1:c.-308+252…

XM_047432308.1:c.-308+25239G>C

N/A Intron Variant
MGA transcript variant X1 XM_005254243.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X6 XM_005254249.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X13 XM_005254252.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X16 XM_005254253.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X41 XM_005254254.5:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X3 XM_006720443.5:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X9 XM_011521397.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X10 XM_011521398.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X42 XM_011521399.4:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X5 XM_047432278.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X12 XM_047432282.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X14 XM_047432283.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X15 XM_047432285.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X18 XM_047432287.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X20 XM_047432289.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X21 XM_047432290.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X23 XM_047432292.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X24 XM_047432293.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X26 XM_047432296.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X27 XM_047432297.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X43 XM_047432309.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X44 XM_047432310.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X45 XM_047432311.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X46 XM_047432312.1:c. N/A Genic Upstream Transcript Variant
MGA transcript variant X47 XM_047432313.1:c. N/A Genic 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 G= C
GRCh38.p14 chr 15 NC_000015.10:g.41646537= NC_000015.10:g.41646537G>C
GRCh37.p13 chr 15 NC_000015.9:g.41938735= NC_000015.9:g.41938735G>C
MGA transcript variant 8 NM_001400246.1:c.-67-22291= NM_001400246.1:c.-67-22291G>C
MGA transcript variant 9 NM_001400247.1:c.-67-22291= NM_001400247.1:c.-67-22291G>C
MGA transcript variant X2 XM_005254246.1:c.-67-22291= XM_005254246.1:c.-67-22291G>C
MGA transcript variant X2 XM_005254246.4:c.-67-22291= XM_005254246.4:c.-67-22291G>C
MGA transcript variant X6 XM_005254247.1:c.-67-22291= XM_005254247.1:c.-67-22291G>C
MGA transcript variant X30 XM_006720445.5:c.-308+25239= XM_006720445.5:c.-308+25239G>C
MGA transcript variant X29 XM_017022029.3:c.-308+24948= XM_017022029.3:c.-308+24948G>C
MGA transcript variant X4 XM_047432276.1:c.-67-22291= XM_047432276.1:c.-67-22291G>C
MGA transcript variant X7 XM_047432279.1:c.-67-22291= XM_047432279.1:c.-67-22291G>C
MGA transcript variant X8 XM_047432280.1:c.-67-22291= XM_047432280.1:c.-67-22291G>C
MGA transcript variant X11 XM_047432281.1:c.-67-22291= XM_047432281.1:c.-67-22291G>C
MGA transcript variant X17 XM_047432286.1:c.-67-22291= XM_047432286.1:c.-67-22291G>C
MGA transcript variant X19 XM_047432288.1:c.-67-22291= XM_047432288.1:c.-67-22291G>C
MGA transcript variant X22 XM_047432291.1:c.-67-22291= XM_047432291.1:c.-67-22291G>C
MGA transcript variant X25 XM_047432295.1:c.-67-22291= XM_047432295.1:c.-67-22291G>C
MGA transcript variant X28 XM_047432298.1:c.-67-22291= XM_047432298.1:c.-67-22291G>C
MGA transcript variant X31 XM_047432299.1:c.-308+25239= XM_047432299.1:c.-308+25239G>C
MGA transcript variant X32 XM_047432300.1:c.-308+24948= XM_047432300.1:c.-308+24948G>C
MGA transcript variant X33 XM_047432301.1:c.-308+25239= XM_047432301.1:c.-308+25239G>C
MGA transcript variant X34 XM_047432302.1:c.-308+24948= XM_047432302.1:c.-308+24948G>C
MGA transcript variant X35 XM_047432303.1:c.-308+25239= XM_047432303.1:c.-308+25239G>C
MGA transcript variant X36 XM_047432304.1:c.-308+25239= XM_047432304.1:c.-308+25239G>C
MGA transcript variant X37 XM_047432305.1:c.-308+25239= XM_047432305.1:c.-308+25239G>C
MGA transcript variant X38 XM_047432306.1:c.-308+25239= XM_047432306.1:c.-308+25239G>C
MGA transcript variant X39 XM_047432307.1:c.-308+25239= XM_047432307.1:c.-308+25239G>C
MGA transcript variant X40 XM_047432308.1:c.-308+25239= XM_047432308.1:c.-308+25239G>C
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#.

14 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss464127353 Sep 17, 2011 (135)
2 1000GENOMES ss1353184008 Aug 21, 2014 (142)
3 GRF ss2701205704 Nov 08, 2017 (151)
4 EVA ss3752999506 Jul 13, 2019 (153)
5 KRGDB ss3931913563 Apr 27, 2020 (154)
6 KOGIC ss3976000623 Apr 27, 2020 (154)
7 GNOMAD ss4287525006 Apr 27, 2021 (155)
8 TOPMED ss4988860413 Apr 27, 2021 (155)
9 TOMMO_GENOMICS ss5215861796 Apr 27, 2021 (155)
10 1000G_HIGH_COVERAGE ss5298198123 Oct 17, 2022 (156)
11 EVA ss5418788037 Oct 17, 2022 (156)
12 1000G_HIGH_COVERAGE ss5599475409 Oct 17, 2022 (156)
13 TOMMO_GENOMICS ss5769568430 Oct 17, 2022 (156)
14 EVA ss5875597521 Oct 17, 2022 (156)
15 1000Genomes NC_000015.9 - 41938735 Oct 12, 2018 (152)
16 1000Genomes_30x NC_000015.10 - 41646537 Oct 17, 2022 (156)
17 gnomAD - Genomes NC_000015.10 - 41646537 Apr 27, 2021 (155)
18 KOREAN population from KRGDB NC_000015.9 - 41938735 Apr 27, 2020 (154)
19 Korean Genome Project NC_000015.10 - 41646537 Apr 27, 2020 (154)
20 8.3KJPN NC_000015.9 - 41938735 Apr 27, 2021 (155)
21 14KJPN NC_000015.10 - 41646537 Oct 17, 2022 (156)
22 TopMed NC_000015.10 - 41646537 Apr 27, 2021 (155)
23 ALFA NC_000015.10 - 41646537 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
66245694, 39090957, 73831103, ss464127353, ss1353184008, ss2701205704, ss3752999506, ss3931913563, ss5215861796, ss5418788037 NC_000015.9:41938734:G:C NC_000015.10:41646536:G:C (self)
87001344, 466976067, 32378624, 103405534, 204406073, 7891890883, ss3976000623, ss4287525006, ss4988860413, ss5298198123, ss5599475409, ss5769568430, ss5875597521 NC_000015.10:41646536:G:C NC_000015.10:41646536:G:C (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 rs183951113

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