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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.

rs28358584

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:3480 (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=0.09381 (7021/74844, ALFA)
G=0.0001 (1/8380, 8.3KJPN)
G=0.0251 (52/2074, HGDP_Stanford) (+ 3 more)
G=0.0363 (40/1102, Daghestan)
G=0.071 (38/534, MGP)
A=0.00 (0/14, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MT-ND1 : Synonymous Variant
MT-ND2 : 2KB Upstream Variant
Publications
0 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-ND2, mitochondrially encoded NADH dehydrogenase 2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.3480A>G K [AAA] > K [AAG] Coding Sequence Variant
NADH dehydrogenase subunit 1 YP_003024026.1:p.Lys58= K (Lys) > K (Lys) Synonymous Variant
MT NC_012920.1:m.3480A>G N/A N/A
Gene: MT-ND1, mitochondrially encoded NADH dehydrogenase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.3480A>G K [AAA] > K [AAG] Coding Sequence Variant
NADH dehydrogenase subunit 1 YP_003024026.1:p.Lys58= K (Lys) > K (Lys) Synonymous Variant
MT NC_012920.1:m.3480A>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 (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 74844 A=0.90619 G=0.09381
European Sub 65718 A=0.90035 G=0.09965
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 3214 A=0.9919 G=0.0081
East Asian Sub 2586 A=0.9977 G=0.0023
Other Asian Sub 628 A=0.968 G=0.032
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 3308 A=0.8912 G=0.1088


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
8.3KJPN JAPANESE Study-wide 8380 A=0.9999 G=0.0001
HGDP-CEPH-db Supplement 1 Global Study-wide 2074 A=0.9749 G=0.0251
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.990 G=0.010
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.897 G=0.103
HGDP-CEPH-db Supplement 1 Europe Sub 316 A=0.962 G=0.038
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 212 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 70 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1102 A=0.9637 G=0.0363
Genome-wide autozygosity in Daghestan Daghestan Sub 622 A=0.965 G=0.035
Genome-wide autozygosity in Daghestan Near_East Sub 140 A=0.943 G=0.057
Genome-wide autozygosity in Daghestan Central Asia Sub 110 A=1.000 G=0.000
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.907 G=0.093
Genome-wide autozygosity in Daghestan South Asian Sub 88 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 34 A=1.00 G=0.00
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.929 G=0.071
SGDP_PRJ Global Study-wide 14 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.3480= NC_012920.1:m.3480A>G
NADH dehydrogenase subunit 1 YP_003024026.1:p.Lys58= YP_003024026.1:p.Lys58=
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#.

25 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35414125 May 24, 2005 (125)
2 BROAD ss37044373 May 24, 2005 (125)
3 ILLUMINA ss66863444 Nov 29, 2006 (127)
4 ILLUMINA ss66931978 Nov 29, 2006 (127)
5 ILLUMINA ss68074752 Dec 12, 2006 (127)
6 PERLEGEN ss69268933 May 16, 2007 (127)
7 ILLUMINA ss70458804 May 25, 2008 (130)
8 ILLUMINA ss70979344 May 16, 2007 (127)
9 ILLUMINA ss75893162 Dec 07, 2007 (129)
10 ILLUMINA ss152536635 Jul 15, 2010 (132)
11 ILLUMINA ss159102676 Jul 15, 2010 (132)
12 ILLUMINA ss169133848 Jul 15, 2010 (132)
13 ILLUMINA ss410884122 Sep 27, 2011 (147)
14 SSMP ss662652559 May 31, 2013 (142)
15 ILLUMINA ss832615472 Jul 14, 2019 (153)
16 HAMMER_LAB ss1397805405 Oct 12, 2018 (152)
17 EVA_MGP ss1711594617 Jul 19, 2016 (147)
18 AFFY ss2986125506 Oct 12, 2018 (152)
19 SWEGEN ss3020998563 Oct 12, 2018 (152)
20 ILLUMINA ss3022981273 Oct 12, 2018 (152)
21 ILLUMINA ss3653538789 Oct 12, 2018 (152)
22 ILLUMINA ss3726656077 Jul 14, 2019 (153)
23 HGDP ss3847966391 Apr 27, 2020 (154)
24 SGDP_PRJ ss3892818866 Apr 27, 2020 (154)
25 TOMMO_GENOMICS ss5236850444 Apr 27, 2021 (155)
26 Genome-wide autozygosity in Daghestan NC_001807.4 - 3481 Apr 27, 2020 (154)
27 HGDP-CEPH-db Supplement 1 NC_001807.4 - 3481 Apr 27, 2020 (154)
28 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 3480 Apr 27, 2020 (154)
29 SGDP_PRJ NC_012920.1 - 3480 Apr 27, 2020 (154)
30 8.3KJPN NC_012920.1 - 3480 Apr 27, 2021 (155)
31 ALFA NC_012920.1 - 3480 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)
rs193303023 Feb 12, 2016 (147)
rs373170727 Aug 21, 2014 (142)
rs386828908 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
542975, 644283, ss35414125, ss37044373, ss66863444, ss66931978, ss68074752, ss69268933, ss70458804, ss70979344, ss75893162, ss662652559, ss832615472, ss1397805405, ss3847966391 NC_001807.4:3480:A:G NC_012920.1:3479:A:G (self)
710377, 44835846, 94819751, 7148473399, ss152536635, ss159102676, ss169133848, ss410884122, ss1711594617, ss2986125506, ss3020998563, ss3022981273, ss3653538789, ss3726656077, ss3892818866, ss5236850444 NC_012920.1:3479:A:G NC_012920.1:3479: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.

No publications for rs28358584

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