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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.

rs28358280

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:10550 (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=0.09361 (8529/91114, ALFA)
G=0.0000 (0/2034, HGDP_Stanford)
G=0.039 (21/534, MGP) (+ 1 more)
A=0.00 (0/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MT-ND4L : Synonymous Variant
MT-ND3 : 500B Downstream Variant
MT-ND4 : 2KB Upstream Variant (+ 1 more)
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-ND3, mitochondrially encoded NADH dehydrogenase 3 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G M [ATA] > M [ATG] Coding Sequence Variant
NADH dehydrogenase subunit 4L YP_003024034.1:p.Met27= M (Met) > M (Met) Synonymous Variant
MT NC_012920.1:m.10550A>G 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.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G M [ATA] > M [ATG] Coding Sequence Variant
NADH dehydrogenase subunit 4L YP_003024034.1:p.Met27= M (Met) > M (Met) Synonymous Variant
MT NC_012920.1:m.10550A>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.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G M [ATA] > M [ATG] Coding Sequence Variant
NADH dehydrogenase subunit 4L YP_003024034.1:p.Met27= M (Met) > M (Met) Synonymous Variant
MT NC_012920.1:m.10550A>G N/A N/A
Gene: MT-ND4L, mitochondrially encoded NADH 4L dehydrogenase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G N/A N/A
MT NC_012920.1:m.10550A>G M [ATA] > M [ATG] Coding Sequence Variant
NADH dehydrogenase subunit 4L YP_003024034.1:p.Met27= M (Met) > M (Met) Synonymous Variant
MT NC_012920.1:m.10550A>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.

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 91114 A=0.90639 G=0.09361
European Sub 81718 A=0.90120 G=0.09880
African Sub 1820 A=0.9593 G=0.0407
African Others Sub 60 A=1.00 G=0.00
African American Sub 1760 A=0.9580 G=0.0420
Asian Sub 3258 A=1.0000 G=0.0000
East Asian Sub 2632 A=1.0000 G=0.0000
Other Asian Sub 626 A=1.000 G=0.000
Latin American 1 Sub 290 A=0.972 G=0.028
Latin American 2 Sub 318 A=0.987 G=0.013
South Asian Sub 176 A=1.000 G=0.000
Other Sub 3534 A=0.8956 G=0.1044


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
HGDP-CEPH-db Supplement 1 Global Study-wide 2034 A=1.0000 G=0.0000
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 410 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Middle_Est Sub 318 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Europe Sub 306 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Africa Sub 242 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
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.961 G=0.039
SGDP_PRJ Global Study-wide 12 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.10550= NC_012920.1:m.10550A>G
NADH dehydrogenase subunit 4L YP_003024034.1:p.Met27= YP_003024034.1:p.Met27=
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#.

33 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35286370 May 24, 2005 (125)
2 BROAD ss37044430 May 24, 2005 (125)
3 ILLUMINA ss66863423 Nov 30, 2006 (127)
4 ILLUMINA ss66931936 Nov 30, 2006 (127)
5 ILLUMINA ss68074731 Dec 12, 2006 (127)
6 ILLUMINA ss70458785 May 26, 2008 (130)
7 ILLUMINA ss70979325 May 17, 2007 (127)
8 ILLUMINA ss75910263 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss105106187 Feb 06, 2009 (130)
10 ILLUMINA ss152536544 Dec 01, 2009 (131)
11 ILLUMINA ss159102659 Dec 01, 2009 (131)
12 ILLUMINA ss169133591 Jul 04, 2010 (135)
13 ILLUMINA ss410884031 Sep 27, 2011 (147)
14 ILLUMINA ss479152845 May 04, 2012 (137)
15 ILLUMINA ss484376860 May 04, 2012 (142)
16 ILLUMINA ss536559234 Jul 19, 2016 (147)
17 ILLUMINA ss782634725 Oct 12, 2018 (152)
18 ILLUMINA ss832615455 Jul 14, 2019 (153)
19 ILLUMINA ss836124373 Oct 12, 2018 (152)
20 EVA_MGP ss1711594869 Jul 19, 2016 (147)
21 ILLUMINA ss1958161339 Jul 19, 2016 (147)
22 ILLUMINA ss2711176115 Oct 12, 2018 (152)
23 AFFY ss2986125582 Oct 12, 2018 (152)
24 SWEGEN ss3020999178 Oct 12, 2018 (152)
25 ILLUMINA ss3022981620 Oct 12, 2018 (152)
26 ILLUMINA ss3625994523 Oct 12, 2018 (152)
27 ILLUMINA ss3645007211 Oct 12, 2018 (152)
28 ILLUMINA ss3653539030 Oct 12, 2018 (152)
29 ILLUMINA ss3726656325 Jul 14, 2019 (153)
30 ILLUMINA ss3744327172 Jul 14, 2019 (153)
31 HGDP ss3847966464 Apr 27, 2020 (154)
32 SGDP_PRJ ss3892819574 Apr 27, 2020 (154)
33 EVA ss5237630426 Apr 27, 2021 (155)
34 HGDP-CEPH-db Supplement 1 NC_001807.4 - 10551 Apr 27, 2020 (154)
35 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 10550 Apr 27, 2020 (154)
36 SGDP_PRJ NC_012920.1 - 10550 Apr 27, 2020 (154)
37 ALFA NC_012920.1 - 10550 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).

Associated ID History Updated (Build)
rs112634840 Sep 17, 2011 (135)
rs193302932 Feb 12, 2016 (147)
rs201707078 Aug 21, 2014 (142)
rs386508192 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644356, ss35286370, ss37044430, ss66863423, ss66931936, ss68074731, ss70458785, ss70979325, ss75910263, ss479152845, ss782634725, ss832615455, ss836124373, ss3847966464 NC_001807.4:10550:A:G NC_012920.1:10549:A:G (self)
710629, 44836554, 15686803930, ss105106187, ss152536544, ss159102659, ss169133591, ss410884031, ss484376860, ss536559234, ss1711594869, ss1958161339, ss2711176115, ss2986125582, ss3020999178, ss3022981620, ss3625994523, ss3645007211, ss3653539030, ss3726656325, ss3744327172, ss3892819574, ss5237630426 NC_012920.1:10549:A:G NC_012920.1:10549: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 rs28358280
PMID Title Author Year Journal
25153900 Mitochondrial genetic variants identified to be associated with BMI in adults. Flaquer A et al. 2014 PloS one
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