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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.

rs28359175

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:13263 (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=0.00712 (530/74386, ALFA)
G=0.0087 (73/8380, 8.3KJPN)
G=0.0307 (90/2930, KOREAN) (+ 5 more)
G=0.0603 (124/2058, HGDP_Stanford)
G=0.0194 (22/1136, Daghestan)
G=0.061 (48/792, PRJEB37584)
G=0.007 (4/534, MGP)
A=0.00 (0/34, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MT-ND5 : Synonymous Variant
MT-CYB : 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-CYB, mitochondrially encoded cytochrome b (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.13263A>G N/A N/A
MT NC_012920.1:m.13263A>G Q [CAA] > Q [CAG] Coding Sequence Variant
NADH dehydrogenase subunit 5 YP_003024036.1:p.Gln309= Q (Gln) > Q (Gln) Synonymous Variant
Gene: MT-ND5, mitochondrially encoded NADH dehydrogenase 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.13263A>G N/A N/A
MT NC_012920.1:m.13263A>G Q [CAA] > Q [CAG] Coding Sequence Variant
NADH dehydrogenase subunit 5 YP_003024036.1:p.Gln309= Q (Gln) > Q (Gln) Synonymous 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.

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 74386 A=0.99288 G=0.00712
European Sub 65732 A=0.99455 G=0.00545
African Sub 1394 A=0.9900 G=0.0100
African Others Sub 60 A=1.00 G=0.00
African American Sub 1334 A=0.9895 G=0.0105
Asian Sub 3216 A=0.9838 G=0.0162
East Asian Sub 2586 A=0.9807 G=0.0193
Other Asian Sub 630 A=0.997 G=0.003
Latin American 1 Sub 290 A=0.979 G=0.021
Latin American 2 Sub 318 A=0.818 G=0.182
South Asian Sub 176 A=1.000 G=0.000
Other Sub 3260 A=0.9871 G=0.0129


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=0.9913 G=0.0087
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.9693 G=0.0307
HGDP-CEPH-db Supplement 1 Global Study-wide 2058 A=0.9397 G=0.0603
HGDP-CEPH-db Supplement 1 Est_Asia Sub 466 A=0.880 G=0.120
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 412 A=0.976 G=0.024
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Europe Sub 312 A=0.994 G=0.006
HGDP-CEPH-db Supplement 1 Africa Sub 234 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 212 A=0.736 G=0.264
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.9806 G=0.0194
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.987 G=0.013
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.972 G=0.028
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.918 G=0.082
Genome-wide autozygosity in Daghestan Europe Sub 108 A=1.000 G=0.000
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=1.00 G=0.00
CNV burdens in cranial meningiomas Global Study-wide 792 A=0.939 G=0.061
CNV burdens in cranial meningiomas CRM Sub 792 A=0.939 G=0.061
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.993 G=0.007
SGDP_PRJ Global Study-wide 34 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.13263= NC_012920.1:m.13263A>G
NADH dehydrogenase subunit 5 YP_003024036.1:p.Gln309= YP_003024036.1:p.Gln309=
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#.

34 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 BROAD ss37044445 May 24, 2005 (125)
2 ILLUMINA ss66863429 Dec 02, 2006 (127)
3 ILLUMINA ss66931948 Dec 02, 2006 (127)
4 ILLUMINA ss68074737 Dec 12, 2006 (127)
5 PERLEGEN ss69268971 May 18, 2007 (127)
6 ILLUMINA ss70458791 May 23, 2008 (130)
7 ILLUMINA ss70979331 May 18, 2007 (127)
8 ILLUMINA ss75879170 Dec 07, 2007 (129)
9 ILLUMINA ss152536568 Dec 01, 2009 (131)
10 ILLUMINA ss159102664 Dec 01, 2009 (131)
11 ILLUMINA ss169133667 Jul 04, 2010 (135)
12 ILLUMINA ss410884060 Sep 27, 2011 (147)
13 ILLUMINA ss479152850 May 04, 2012 (137)
14 ILLUMINA ss484376871 May 04, 2012 (142)
15 ILLUMINA ss536559239 Jul 19, 2016 (147)
16 ILLUMINA ss782634730 Oct 12, 2018 (152)
17 ILLUMINA ss832615460 Jul 14, 2019 (153)
18 ILLUMINA ss836124378 Oct 12, 2018 (152)
19 HAMMER_LAB ss1397805555 Oct 12, 2018 (152)
20 EVA_MGP ss1711594978 Jul 19, 2016 (147)
21 ILLUMINA ss1958161405 Jul 19, 2016 (147)
22 AFFY ss2986125606 Oct 12, 2018 (152)
23 ILLUMINA ss3022981779 Oct 12, 2018 (152)
24 ILLUMINA ss3625994552 Oct 12, 2018 (152)
25 ILLUMINA ss3645007263 Oct 12, 2018 (152)
26 ILLUMINA ss3653539174 Oct 12, 2018 (152)
27 ILLUMINA ss3726656489 Jul 14, 2019 (153)
28 ILLUMINA ss3744327201 Jul 14, 2019 (153)
29 HGDP ss3847966487 Apr 27, 2020 (154)
30 SGDP_PRJ ss3892819798 Apr 27, 2020 (154)
31 KRGDB ss3892821990 Apr 27, 2020 (154)
32 EVA ss3984773893 Apr 27, 2021 (155)
33 TOMMO_GENOMICS ss5236852453 Apr 27, 2021 (155)
34 EVA ss5237630447 Apr 27, 2021 (155)
35 Genome-wide autozygosity in Daghestan NC_001807.4 - 13264 Apr 27, 2020 (154)
36 HGDP-CEPH-db Supplement 1 NC_001807.4 - 13264 Apr 27, 2020 (154)
37 KOREAN population from KRGDB NC_001807.4 - 13264 Apr 27, 2020 (154)
38 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 13263 Apr 27, 2020 (154)
39 CNV burdens in cranial meningiomas NC_012920.1 - 13263 Apr 27, 2021 (155)
40 SGDP_PRJ NC_012920.1 - 13263 Apr 27, 2020 (154)
41 8.3KJPN NC_012920.1 - 13263 Apr 27, 2021 (155)
42 ALFA NC_012920.1 - 13263 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)
rs113496490 Sep 17, 2011 (135)
rs193302961 Feb 12, 2016 (147)
rs201343131 Aug 21, 2014 (142)
rs386508194 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
543121, 644379, 50801040, ss37044445, ss66863429, ss66931948, ss68074737, ss69268971, ss70458791, ss70979331, ss75879170, ss479152850, ss782634730, ss832615460, ss836124378, ss1397805555, ss3847966487, ss3892821990 NC_001807.4:13263:A:G NC_012920.1:13262:A:G (self)
710738, 312594, 44836778, 94821760, 16964949371, ss152536568, ss159102664, ss169133667, ss410884060, ss484376871, ss536559239, ss1711594978, ss1958161405, ss2986125606, ss3022981779, ss3625994552, ss3645007263, ss3653539174, ss3726656489, ss3744327201, ss3892819798, ss3984773893, ss5236852453, ss5237630447 NC_012920.1:13262:A:G NC_012920.1:13262: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 rs28359175

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