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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs2853826

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrMT:10398 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.16946 (12337/72802, ALFA)
A=0.29089 (4110/14129, 14KJPN)
A=0.2889 (2421/8380, 8.3KJPN) (+ 3 more)
A=0.199 (141/710, PRJEB37584)
G=0.066 (35/534, MGP)
A=0.000 (0/304, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-ND3 : Missense Variant
MT-CO3 : 500B Downstream Variant
MT-ND4 : 2KB Upstream Variant (+ 2 more)
MT-ND4L : 2KB Upstream Variant
MT-ND5 : 2KB Upstream Variant
Publications
8 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 72802 A=0.83043 G=0.16946, T=0.00011
European Sub 66440 A=0.84846 G=0.15144, T=0.00009
African Sub 1288 A=0.3851 G=0.6134, T=0.0016
African Others Sub 18 A=0.56 G=0.44, T=0.00
African American Sub 1270 A=0.3827 G=0.6157, T=0.0016
Asian Sub 138 A=0.420 G=0.580, T=0.000
East Asian Sub 82 A=0.39 G=0.61, T=0.00
Other Asian Sub 56 A=0.46 G=0.54, T=0.00
Latin American 1 Sub 16 A=0.62 G=0.38, T=0.00
Latin American 2 Sub 90 A=0.87 G=0.13, T=0.00
South Asian Sub 16 A=1.00 G=0.00, T=0.00
Other Sub 4814 A=0.7119 G=0.2881, T=0.0000


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
Allele Frequency Aggregator Total Global 72802 A=0.83043 G=0.16946, T=0.00011
Allele Frequency Aggregator European Sub 66440 A=0.84846 G=0.15144, T=0.00009
Allele Frequency Aggregator Other Sub 4814 A=0.7119 G=0.2881, T=0.0000
Allele Frequency Aggregator African Sub 1288 A=0.3851 G=0.6134, T=0.0016
Allele Frequency Aggregator Asian Sub 138 A=0.420 G=0.580, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 90 A=0.87 G=0.13, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 16 A=0.62 G=0.38, T=0.00
Allele Frequency Aggregator South Asian Sub 16 A=1.00 G=0.00, T=0.00
14KJPN JAPANESE Study-wide 14129 A=0.29089 G=0.70911
8.3KJPN JAPANESE Study-wide 8380 A=0.2889 G=0.7111
CNV burdens in cranial meningiomas Global Study-wide 710 A=0.199 G=0.801
CNV burdens in cranial meningiomas CRM Sub 710 A=0.199 G=0.801
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.934 G=0.066
SGDP_PRJ Global Study-wide 304 A=0.000 G=1.000
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.

Gene: MT-CO3, mitochondrially encoded cytochrome c oxidase III (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G T [ACC] > A [GCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T T [ACC] > S [TCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ser T (Thr) > S (Ser) Missense Variant
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
Gene: MT-ND4, mitochondrially encoded NADH dehydrogenase 4 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G T [ACC] > A [GCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T T [ACC] > S [TCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ser T (Thr) > S (Ser) Missense Variant
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
Gene: MT-ND4L, mitochondrially encoded NADH 4L dehydrogenase (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G T [ACC] > A [GCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T T [ACC] > S [TCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ser T (Thr) > S (Ser) Missense Variant
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
Gene: MT-ND5, mitochondrially encoded NADH dehydrogenase 5 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G T [ACC] > A [GCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T T [ACC] > S [TCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ser T (Thr) > S (Ser) Missense Variant
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
Gene: MT-ND3, mitochondrially encoded NADH dehydrogenase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G T [ACC] > A [GCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>G N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T T [ACC] > S [TCC] Coding Sequence Variant
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114Ser T (Thr) > S (Ser) Missense Variant
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
MT NC_012920.1:m.10398A>T N/A N/A
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.

Allele: G (allele ID: 24752 )
ClinVar Accession Disease Names Clinical Significance
RCV000010359.3 Parkinson disease, resistance to Protective
RCV000854647.1 Leigh syndrome Benign
Allele: T (allele ID: 680178 )
ClinVar Accession Disease Names Clinical Significance
RCV000854648.1 Leigh syndrome Likely-Benign
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 A= G T
MT NC_012920.1:m.10398= NC_012920.1:m.10398A>G NC_012920.1:m.10398A>T
NADH dehydrogenase subunit 3 YP_003024033.1:p.Thr114= YP_003024033.1:p.Thr114Ala YP_003024033.1:p.Thr114Ser
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#.

64 SubSNP, 6 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1420552 Oct 10, 2002 (124)
2 SC_JCM ss4040518 Sep 28, 2001 (100)
3 TSC-CSHL ss5583627 Oct 10, 2002 (124)
4 SSAHASNP ss35452962 May 24, 2005 (125)
5 BROAD ss46525711 Mar 14, 2006 (126)
6 ILLUMINA ss66863501 Nov 30, 2006 (127)
7 ILLUMINA ss66932092 Nov 30, 2006 (127)
8 ILLUMINA ss68074809 Dec 12, 2006 (127)
9 ILLUMINA ss70458858 May 25, 2008 (130)
10 ILLUMINA ss70979398 May 17, 2007 (127)
11 ILLUMINA ss75913112 Dec 07, 2007 (130)
12 AFFY ss76713320 Dec 07, 2007 (132)
13 BCMHGSC_JDW ss94206217 Mar 25, 2008 (129)
14 ILLUMINA ss152536854 Dec 01, 2009 (132)
15 ILLUMINA ss159102717 Dec 01, 2009 (132)
16 COMPLETE_GENOMICS ss165985487 Jul 04, 2010 (135)
17 ILLUMINA ss169134477 Dec 03, 2013 (138)
18 ILLUMINA ss479152885 May 04, 2012 (137)
19 ILLUMINA ss484376939 May 04, 2012 (136)
20 EXOME_CHIP ss491581430 May 04, 2012 (137)
21 OMIM-CURATED-RECORDS ss510059373 Apr 11, 2012 (136)
22 ILLUMINA ss532727987 Jul 19, 2016 (147)
23 ILLUMINA ss536559289 Jul 19, 2016 (147)
24 TISHKOFF ss567118020 Apr 25, 2013 (138)
25 ILLUMINA ss778657311 Jul 19, 2016 (147)
26 ILLUMINA ss780683994 Jul 19, 2016 (147)
27 ILLUMINA ss782634765 Oct 12, 2018 (152)
28 ILLUMINA ss783357417 Jul 19, 2016 (147)
29 ILLUMINA ss832615513 Jul 14, 2019 (153)
30 ILLUMINA ss834115302 Jul 19, 2016 (147)
31 ILLUMINA ss836124409 Oct 12, 2018 (152)
32 EVA_MGP ss1711594865 Jul 19, 2016 (147)
33 ILLUMINA ss1752791115 Jul 19, 2016 (147)
34 ILLUMINA ss1917715452 Jul 19, 2016 (147)
35 ILLUMINA ss1945966502 Jul 19, 2016 (147)
36 ILLUMINA ss1945966503 Jul 19, 2016 (147)
37 ILLUMINA ss1958161336 Jul 19, 2016 (147)
38 TMC_SNPDB ss1997225866 Jul 19, 2016 (147)
39 ILLUMINA ss2634932640 Oct 12, 2018 (152)
40 GRF ss2710056330 Oct 12, 2018 (152)
41 ILLUMINA ss2711176113 Oct 12, 2018 (152)
42 AFFY ss2986125579 Oct 12, 2018 (152)
43 SWEGEN ss3020999167 Oct 12, 2018 (152)
44 ILLUMINA ss3022981615 Oct 12, 2018 (152)
45 ILLUMINA ss3630385182 Oct 12, 2018 (152)
46 ILLUMINA ss3630385183 Oct 12, 2018 (152)
47 ILLUMINA ss3632820200 Oct 12, 2018 (152)
48 ILLUMINA ss3635240400 Oct 12, 2018 (152)
49 ILLUMINA ss3640947790 Oct 12, 2018 (152)
50 ILLUMINA ss3653539025 Oct 12, 2018 (152)
51 ILLUMINA ss3726656319 Jul 14, 2019 (153)
52 ILLUMINA ss3744596942 Jul 14, 2019 (153)
53 ILLUMINA ss3745540369 Jul 14, 2019 (153)
54 ILLUMINA ss3773032089 Jul 14, 2019 (153)
55 HGDP ss3847966462 Apr 27, 2020 (154)
56 SGDP_PRJ ss3892819563 Apr 27, 2020 (154)
57 KRGDB ss3892821625 Apr 27, 2020 (154)
58 EVA ss3984773810 Apr 27, 2021 (155)
59 TOMMO_GENOMICS ss5236851911 Apr 27, 2021 (155)
60 SANFORD_IMAGENETICS ss5624733825 Oct 13, 2022 (156)
61 SANFORD_IMAGENETICS ss5666160653 Oct 13, 2022 (156)
62 TOMMO_GENOMICS ss5799399882 Oct 13, 2022 (156)
63 YY_MCH ss5819540333 Oct 13, 2022 (156)
64 EVA ss5848225865 Oct 13, 2022 (156)
65 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 10398 Apr 27, 2020 (154)
66 CNV burdens in cranial meningiomas NC_012920.1 - 10398 Apr 27, 2021 (155)
67 SGDP_PRJ NC_012920.1 - 10398 Apr 27, 2020 (154)
68 8.3KJPN NC_012920.1 - 10398 Apr 27, 2021 (155)
69 14KJPN NC_012920.1 - 10398 Oct 13, 2022 (156)
70 ALFA NC_012920.1 - 10398 Apr 27, 2021 (155)
71 ClinVar RCV000010359.3 Oct 12, 2018 (152)
72 ClinVar RCV000854647.1 Apr 27, 2020 (154)
73 ClinVar RCV000854648.1 Apr 27, 2020 (154)
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)
rs3899189 Dec 02, 2004 (124)
rs4133677 Apr 21, 2003 (114)
rs56162303 Jul 15, 2010 (132)
rs56189606 May 25, 2008 (130)
rs111408880 Sep 17, 2011 (135)
rs200481026 Aug 06, 2014 (136)
rs386508221 Aug 06, 2014 (136)
rs386829100 Aug 06, 2014 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35452962, ss76713320, ss94206217, ss479152885, ss782634765, ss832615513, ss836124409, ss3847966462, ss3892821625 NC_001807.4:10398:G:G NC_012920.1:10397:A:G (self)
RCV000010359.3, RCV000854647.1, 710625, 312511, 44836543, 94821218, 133236986, 7991533491, ss1420552, ss4040518, ss5583627, ss46525711, ss66863501, ss66932092, ss68074809, ss70458858, ss70979398, ss75913112, ss152536854, ss159102717, ss165985487, ss169134477, ss484376939, ss491581430, ss510059373, ss532727987, ss536559289, ss567118020, ss778657311, ss780683994, ss783357417, ss834115302, ss1711594865, ss1752791115, ss1917715452, ss1945966502, ss1945966503, ss1958161336, ss1997225866, ss2634932640, ss2710056330, ss2711176113, ss2986125579, ss3020999167, ss3022981615, ss3630385182, ss3630385183, ss3632820200, ss3635240400, ss3640947790, ss3653539025, ss3726656319, ss3744596942, ss3745540369, ss3773032089, ss3892819563, ss3984773810, ss5236851911, ss5624733825, ss5666160653, ss5799399882, ss5819540333, ss5848225865 NC_012920.1:10397:A:G NC_012920.1:10397:A:G (self)
RCV000854648.1, 7991533491 NC_012920.1:10397:A:T NC_012920.1:10397:A:T (self)
Help

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

8 citations for rs2853826
PMID Title Author Year Journal
6343397 Assignment of a polymorphic polypeptide to the human mitochondrial DNA unidentified reading frame 3 gene by a new peptide mapping strategy. Oliver NA et al. 1983 The Journal of biological chemistry
17066297 The possible role of 10398A and 16189C mtDNA variants in providing susceptibility to T2DM in two North Indian populations: a replicative study. Bhat A et al. 2007 Human genetics
23133645 The interactive effect of SIRT1 promoter region polymorphism on type 2 diabetes susceptibility in the North Indian population. Rai E et al. 2012 PloS one
24437375 Factors associated with oxidative stress and cancer risk in the Breast and Prostate Cancer Cohort Consortium. Blein S et al. 2014 Free radical research
26116242 Mitochondrial DNA polymorphisms, its copy number change and outcome in colorectal cancer. Mohideen AM et al. 2015 BMC research notes
26336829 Mitochondrial NADH Dehydrogenase Subunit 3 Polymorphism Associated with an Earlier Age at Onset in Male Machado-Joseph disease Patients. Chen S et al. 2016 CNS neuroscience & therapeutics
32396277 Genetic analysis resolves differential diagnosis of a familial syndromic dilated cardiomyopathy: A new case of Alström syndrome. Lombardo B et al. 2020 Molecular genetics & genomic medicine
34120353 Lack of association between single polymorphic variants of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase 3, and 4L (MT-ND3 and MT-ND4L) and male infertility. Dahadhah FW et al. 2021 Andrologia
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

No flank sequence available

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