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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.

rs2853498

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:12308 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.21670 (17272/79704, ALFA)
G=0.1212 (252/2080, HGDP_Stanford)
G=0.005 (4/792, PRJEB37584) (+ 2 more)
G=0.110 (59/534, MGP)
A=0.00 (0/62, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-ND4 : 500B Downstream Variant
MT-ND5 : 2KB Upstream Variant
Publications
1 citation
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.

Gene: MT-ND4, mitochondrially encoded NADH dehydrogenase 4 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.12308A>G N/A N/A
MT NC_012920.1:m.12308A>G 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.12308A>G N/A N/A
MT NC_012920.1:m.12308A>G 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: 677586 )
ClinVar Accession Disease Names Clinical Significance
RCV000851081.1 Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign

ALFA Allele Frequency (New)
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 79704 A=0.78330 G=0.21670
European Sub 69210 A=0.76632 G=0.23368
African Sub 748 A=0.858 G=0.142
African Others Sub 8 A=1.0 G=0.0
African American Sub 740 A=0.857 G=0.143
Asian Sub 3032 A=0.9964 G=0.0036
East Asian Sub 1838 A=0.9956 G=0.0044
Other Asian Sub 1194 A=0.9975 G=0.0025
Latin American 1 Sub 6 A=1.0 G=0.0
Latin American 2 Sub 22 A=1.00 G=0.00
South Asian Sub 0 A=0 G=0
Other Sub 6686 A=0.8531 G=0.1469


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").

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Study Population Group Sample Size Ref Allele Alt Allele
HGDP-CEPH-db Supplement 1 Global Study-wide 2080 A=0.8788 G=0.1212
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=0.996 G=0.004
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.812 G=0.188
HGDP-CEPH-db Supplement 1 Middle_Est Sub 348 A=0.736 G=0.264
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.750 G=0.250
HGDP-CEPH-db Supplement 1 Africa Sub 240 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=1.00 G=0.00
CNV burdens in cranial meningiomas Global Study-wide 792 A=0.995 G=0.005
CNV burdens in cranial meningiomas CRM Sub 792 A=0.995 G=0.005
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.890 G=0.110
SGDP_PRJ Global Study-wide 62 A=0.00 G=1.00
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
MT NC_012920.1:m.12308= NC_012920.1:m.12308A>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, 5 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4040097 Sep 28, 2001 (100)
2 SSAHASNP ss35378314 May 24, 2005 (125)
3 BROAD ss46525726 Mar 14, 2006 (126)
4 ILLUMINA ss66863427 Nov 30, 2006 (127)
5 ILLUMINA ss66931944 Nov 30, 2006 (127)
6 ILLUMINA ss68074735 Dec 12, 2006 (127)
7 ILLUMINA ss70458789 May 23, 2008 (130)
8 ILLUMINA ss70979329 May 17, 2007 (127)
9 ILLUMINA ss75917641 Dec 06, 2007 (129)
10 AFFY ss76713238 Dec 08, 2007 (135)
11 KRIBB_YJKIM ss104882235 Feb 03, 2009 (130)
12 ILLUMINA ss152536558 Dec 01, 2009 (132)
13 ILLUMINA ss159102662 Dec 01, 2009 (132)
14 ILLUMINA ss159849691 Dec 01, 2009 (132)
15 COMPLETE_GENOMICS ss163709876 Jul 04, 2010 (135)
16 ILLUMINA ss169133637 Jul 04, 2010 (135)
17 ILLUMINA ss410884047 Sep 27, 2011 (147)
18 ILLUMINA ss479152848 May 04, 2012 (137)
19 ILLUMINA ss484376867 May 04, 2012 (142)
20 EXOME_CHIP ss491581448 May 04, 2012 (137)
21 ILLUMINA ss536559237 Jul 19, 2016 (147)
22 ILLUMINA ss780683988 Jul 19, 2016 (147)
23 ILLUMINA ss782634728 Oct 12, 2018 (152)
24 ILLUMINA ss783357411 Jul 19, 2016 (147)
25 ILLUMINA ss836124376 Oct 12, 2018 (152)
26 EVA_MGP ss1711594939 Jul 19, 2016 (147)
27 ILLUMINA ss1752791130 Jul 19, 2016 (147)
28 ILLUMINA ss1917715466 Jul 19, 2016 (147)
29 ILLUMINA ss1945966540 Jul 19, 2016 (147)
30 ILLUMINA ss1958161379 Jul 19, 2016 (147)
31 TMC_SNPDB ss1997225876 Jul 19, 2016 (147)
32 ILLUMINA ss2634932664 Oct 12, 2018 (152)
33 ILLUMINA ss2635200882 Oct 12, 2018 (152)
34 ILLUMINA ss2711176128 Oct 12, 2018 (152)
35 AFFY ss2985479575 Oct 12, 2018 (152)
36 SWEGEN ss3020999308 Oct 12, 2018 (152)
37 ILLUMINA ss3022981718 Oct 12, 2018 (152)
38 ILLUMINA ss3630385192 Oct 12, 2018 (152)
39 ILLUMINA ss3635240402 Oct 12, 2018 (152)
40 ILLUMINA ss3640947805 Oct 12, 2018 (152)
41 ILLUMINA ss3645007243 Oct 12, 2018 (152)
42 ILLUMINA ss3653539117 Oct 12, 2018 (152)
43 ILLUMINA ss3654244692 Oct 12, 2018 (152)
44 ILLUMINA ss3726656428 Jul 14, 2019 (153)
45 ILLUMINA ss3744596944 Jul 14, 2019 (153)
46 ILLUMINA ss3745540384 Jul 14, 2019 (153)
47 ILLUMINA ss3773032103 Jul 14, 2019 (153)
48 HGDP ss3847966479 Apr 27, 2020 (154)
49 SGDP_PRJ ss3892819718 Apr 27, 2020 (154)
50 EVA ss3984773860 Apr 27, 2021 (155)
51 EVA ss5237630438 Apr 27, 2021 (155)
52 HGDP-CEPH-db Supplement 1 NC_001807.4 - 12309 Apr 27, 2020 (154)
53 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 12308 Apr 27, 2020 (154)
54 CNV burdens in cranial meningiomas NC_012920.1 - 12308 Apr 27, 2021 (155)
55 SGDP_PRJ NC_012920.1 - 12308 Apr 27, 2020 (154)
56 ALFA NC_012920.1 - 12308 Apr 27, 2021 (155)
57 ClinVar RCV000851081.1 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)
rs56421811 Sep 17, 2011 (135)
rs80307860 Jul 15, 2010 (132)
rs112448012 Sep 17, 2011 (135)
rs112940235 Sep 17, 2011 (135)
rs193302948 Feb 12, 2016 (147)
rs199837011 Aug 21, 2014 (142)
rs377391736 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644371, ss35378314, ss76713238, ss159849691, ss163709876, ss479152848, ss782634728, ss836124376, ss2635200882, ss3847966479 NC_001807.4:12308:A:G NC_012920.1:12307:A:G (self)
RCV000851081.1, 710699, 312561, 44836698, 8207230084, ss4040097, ss46525726, ss66863427, ss66931944, ss68074735, ss70458789, ss70979329, ss75917641, ss104882235, ss152536558, ss159102662, ss169133637, ss410884047, ss484376867, ss491581448, ss536559237, ss780683988, ss783357411, ss1711594939, ss1752791130, ss1917715466, ss1945966540, ss1958161379, ss1997225876, ss2634932664, ss2711176128, ss2985479575, ss3020999308, ss3022981718, ss3630385192, ss3635240402, ss3640947805, ss3645007243, ss3653539117, ss3654244692, ss3726656428, ss3744596944, ss3745540384, ss3773032103, ss3892819718, ss3984773860, ss5237630438 NC_012920.1:12307:A:G NC_012920.1:12307:A:G (self)
Help

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

1 citation for rs2853498
PMID Title Author Year Journal
32799222 [Variability of the Mitochondrial Genome and Development of the Primary Progressing form of Multiple Sclerosis]. Kozin MS et al. 2020 Molekuliarnaia biologiia
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.post596+ae089ad