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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.

rs28357980

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:4917 (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=0.09514 (8147/85630, ALFA)
G=0.0004 (3/8380, 8.3KJPN)
G=0.0007 (2/2922, KOREAN) (+ 4 more)
G=0.0368 (76/2066, HGDP_Stanford)
G=0.001 (1/792, PRJEB37584)
G=0.058 (31/534, MGP)
A=0.0 (0/10, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-ND2 : Missense Variant
MT-CO1 : 2KB Upstream Variant
Publications
3 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.

Gene: MT-CO1, mitochondrially encoded cytochrome c oxidase I (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.4917A>G N/A N/A
MT NC_012920.1:m.4917A>G N [AAC] > D [GAC] Coding Sequence Variant
NADH dehydrogenase subunit 2 YP_003024027.1:p.Asn150Asp N (Asn) > D (Asp) Missense Variant
Gene: MT-ND2, mitochondrially encoded NADH dehydrogenase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.4917A>G N/A N/A
MT NC_012920.1:m.4917A>G N [AAC] > D [GAC] Coding Sequence Variant
NADH dehydrogenase subunit 2 YP_003024027.1:p.Asn150Asp N (Asn) > D (Asp) Missense 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.

Allele: G (allele ID: 24755 )
ClinVar Accession Disease Names Clinical Significance
RCV000010364.1 Leber's optic atrophy Uncertain-Significance
RCV000853834.1 Leigh syndrome 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 85630 A=0.90486 G=0.09514
European Sub 75162 A=0.89794 G=0.10206
African Sub 1466 A=0.9741 G=0.0259
African Others Sub 60 A=1.00 G=0.00
African American Sub 1406 A=0.9730 G=0.0270
Asian Sub 3288 A=0.9982 G=0.0018
East Asian Sub 2632 A=0.9985 G=0.0015
Other Asian Sub 656 A=0.997 G=0.003
Latin American 1 Sub 290 A=0.924 G=0.076
Latin American 2 Sub 318 A=0.981 G=0.019
South Asian Sub 176 A=0.989 G=0.011
Other Sub 4930 A=0.9185 G=0.0815


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
8.3KJPN JAPANESE Study-wide 8380 A=0.9996 G=0.0004
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9993 G=0.0007
HGDP-CEPH-db Supplement 1 Global Study-wide 2066 A=0.9632 G=0.0368
HGDP-CEPH-db Supplement 1 Est_Asia Sub 464 A=0.996 G=0.004
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 408 A=0.966 G=0.034
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.943 G=0.057
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.875 G=0.125
HGDP-CEPH-db Supplement 1 Africa Sub 238 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 214 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=0.999 G=0.001
CNV burdens in cranial meningiomas CRM Sub 792 A=0.999 G=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.942 G=0.058
SGDP_PRJ Global Study-wide 10 A=0.0 G=1.0
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.4917= NC_012920.1:m.4917A>G
NADH dehydrogenase subunit 2 YP_003024027.1:p.Asn150= YP_003024027.1:p.Asn150Asp
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#.

52 SubSNP, 7 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35415088 May 24, 2005 (125)
2 BROAD ss37044389 May 24, 2005 (125)
3 ILLUMINA ss66863450 Nov 29, 2006 (127)
4 ILLUMINA ss66931990 Nov 29, 2006 (127)
5 ILLUMINA ss68074758 Dec 12, 2006 (127)
6 ILLUMINA ss70458810 May 23, 2008 (130)
7 ILLUMINA ss70979350 May 16, 2007 (127)
8 ILLUMINA ss75867526 Dec 06, 2007 (129)
9 ILLUMINA ss152536655 Dec 01, 2009 (131)
10 ILLUMINA ss159102680 Dec 01, 2009 (131)
11 ILLUMINA ss169133907 Jul 04, 2010 (135)
12 ILLUMINA ss479152861 May 04, 2012 (137)
13 ILLUMINA ss484376892 May 04, 2012 (136)
14 EXOME_CHIP ss491581368 May 04, 2012 (137)
15 OMIM-CURATED-RECORDS ss510059363 Apr 11, 2012 (136)
16 ILLUMINA ss536559254 Jul 19, 2016 (147)
17 TISHKOFF ss567117943 Apr 25, 2013 (138)
18 ILLUMINA ss780796959 Jul 19, 2016 (147)
19 ILLUMINA ss782634741 Oct 12, 2018 (152)
20 ILLUMINA ss783478222 Jul 19, 2016 (147)
21 ILLUMINA ss836124387 Oct 12, 2018 (152)
22 EVA_MGP ss1711594666 Jul 19, 2016 (147)
23 ILLUMINA ss1752791279 Jul 19, 2016 (147)
24 ILLUMINA ss1917715415 Jul 19, 2016 (147)
25 ILLUMINA ss1945966383 Jul 19, 2016 (147)
26 ILLUMINA ss1958161233 Jul 19, 2016 (147)
27 ILLUMINA ss1958161234 Jul 19, 2016 (147)
28 ILLUMINA ss2634932565 Oct 12, 2018 (152)
29 ILLUMINA ss2635200862 Oct 12, 2018 (152)
30 ILLUMINA ss2711176056 Oct 12, 2018 (152)
31 AFFY ss2986125534 Oct 12, 2018 (152)
32 SWEGEN ss3020998684 Oct 12, 2018 (152)
33 ILLUMINA ss3022981351 Oct 12, 2018 (152)
34 ILLUMINA ss3022981352 Oct 12, 2018 (152)
35 ILLUMINA ss3022981353 Oct 12, 2018 (152)
36 ILLUMINA ss3625994473 Oct 12, 2018 (152)
37 ILLUMINA ss3640947754 Oct 12, 2018 (152)
38 ILLUMINA ss3645007130 Oct 12, 2018 (152)
39 ILLUMINA ss3645007131 Oct 12, 2018 (152)
40 OMUKHERJEE_ADBS ss3646580217 Oct 12, 2018 (152)
41 ILLUMINA ss3653538843 Oct 12, 2018 (152)
42 ILLUMINA ss3653538844 Oct 12, 2018 (152)
43 ILLUMINA ss3653538845 Oct 12, 2018 (152)
44 ILLUMINA ss3726656135 Jul 14, 2019 (153)
45 ILLUMINA ss3744327121 Jul 14, 2019 (153)
46 ILLUMINA ss3745540334 Jul 14, 2019 (153)
47 ILLUMINA ss3773032053 Jul 14, 2019 (153)
48 HGDP ss3847966409 Apr 27, 2020 (154)
49 SGDP_PRJ ss3892819006 Apr 27, 2020 (154)
50 KRGDB ss3892820845 Apr 27, 2020 (154)
51 EVA ss3984773721 Apr 27, 2021 (155)
52 TOMMO_GENOMICS ss5236850701 Apr 27, 2021 (155)
53 HGDP-CEPH-db Supplement 1 NC_001807.4 - 4918 Apr 27, 2020 (154)
54 KOREAN population from KRGDB NC_001807.4 - 4918 Apr 27, 2020 (154)
55 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 4917 Apr 27, 2020 (154)
56 CNV burdens in cranial meningiomas NC_012920.1 - 4917 Apr 27, 2021 (155)
57 SGDP_PRJ NC_012920.1 - 4917 Apr 27, 2020 (154)
58 8.3KJPN NC_012920.1 - 4917 Apr 27, 2021 (155)
59 ALFA NC_012920.1 - 4917 Apr 27, 2021 (155)
60 ClinVar RCV000010364.1 Oct 12, 2018 (152)
61 ClinVar RCV000853834.1 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)
rs111228224 Sep 17, 2011 (135)
rs201425642 Aug 06, 2014 (136)
rs377450783 Aug 06, 2014 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644301, 50799895, ss35415088, ss479152861, ss782634741, ss836124387, ss2635200862, ss3847966409, ss3892820845 NC_001807.4:4917:A:G NC_012920.1:4916:A:G (self)
RCV000010364.1, RCV000853834.1, 710426, 312421, 44835986, 94820008, 15703418382, ss37044389, ss66863450, ss66931990, ss68074758, ss70458810, ss70979350, ss75867526, ss152536655, ss159102680, ss169133907, ss484376892, ss491581368, ss510059363, ss536559254, ss567117943, ss780796959, ss783478222, ss1711594666, ss1752791279, ss1917715415, ss1945966383, ss1958161233, ss1958161234, ss2634932565, ss2711176056, ss2986125534, ss3020998684, ss3022981351, ss3022981352, ss3022981353, ss3625994473, ss3640947754, ss3645007130, ss3645007131, ss3646580217, ss3653538843, ss3653538844, ss3653538845, ss3726656135, ss3744327121, ss3745540334, ss3773032053, ss3892819006, ss3984773721, ss5236850701 NC_012920.1:4916:A:G NC_012920.1:4916: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.

3 citations for rs28357980
PMID Title Author Year Journal
1900003 Alternative, simultaneous complex I mitochondrial DNA mutations in Leber's hereditary optic neuropathy. Johns DR et al. 1991 Biochemical and biophysical research communications
18461138 Mitochondrial DNA polymorphism A4917G is independently associated with age-related macular degeneration. Canter JA et al. 2008 PloS one
32635923 Mitochondrial GWAS and association of nuclear - mitochondrial epistasis with BMI in T1DM patients. Ludwig-Słomczyńska AH et al. 2020 BMC medical genomics
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