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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.

rs28358586

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:3547 (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=0.0156 (140/8980, ALFA)
G=0.0001 (1/8380, 8.3KJPN)
G=0.0000 (0/2028, HGDP_Stanford) (+ 4 more)
G=0.0018 (2/1098, Daghestan)
G=0.003 (2/758, PRJEB37584)
G=0.017 (9/534, MGP)
A=0.0 (0/10, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-ND1 : Missense 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.3547A>G I [ATC] > V [GTC] Coding Sequence Variant
NADH dehydrogenase subunit 1 YP_003024026.1:p.Ile81Val I (Ile) > V (Val) Missense Variant
MT NC_012920.1:m.3547A>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.3547A>G I [ATC] > V [GTC] Coding Sequence Variant
NADH dehydrogenase subunit 1 YP_003024026.1:p.Ile81Val I (Ile) > V (Val) Missense Variant
MT NC_012920.1:m.3547A>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: 680906 )
ClinVar Accession Disease Names Clinical Significance
RCV000853675.1 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 8980 A=0.9844 G=0.0156
European Sub 6056 A=0.9881 G=0.0119
African Sub 594 A=0.983 G=0.017
African Others Sub 8 A=1.0 G=0.0
African American Sub 586 A=0.983 G=0.017
Asian Sub 56 A=1.00 G=0.00
East Asian Sub 26 A=1.00 G=0.00
Other Asian Sub 30 A=1.00 G=0.00
Latin American 1 Sub 0 A=0 G=0
Latin American 2 Sub 0 A=0 G=0
South Asian Sub 0 A=0 G=0
Other Sub 2274 A=0.9745 G=0.0255


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 2028 A=1.0000 G=0.0000
HGDP-CEPH-db Supplement 1 Est_Asia Sub 452 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 346 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Europe Sub 314 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 192 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1098 A=0.9982 G=0.0018
Genome-wide autozygosity in Daghestan Daghestan Sub 622 A=0.997 G=0.003
Genome-wide autozygosity in Daghestan Near_East Sub 138 A=1.000 G=0.000
Genome-wide autozygosity in Daghestan Europe Sub 108 A=1.000 G=0.000
Genome-wide autozygosity in Daghestan Central Asia Sub 100 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan South Asian Sub 94 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 758 A=0.997 G=0.003
CNV burdens in cranial meningiomas CRM Sub 758 A=0.997 G=0.003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.983 G=0.017
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.3547= NC_012920.1:m.3547A>G
NADH dehydrogenase subunit 1 YP_003024026.1:p.Ile81= YP_003024026.1:p.Ile81Val
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#.

24 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35463095 May 24, 2005 (125)
2 BROAD ss37044375 May 24, 2005 (125)
3 ILLUMINA ss66863445 Dec 01, 2006 (127)
4 ILLUMINA ss66931980 Dec 01, 2006 (127)
5 ILLUMINA ss68074753 Dec 12, 2006 (127)
6 PERLEGEN ss69268935 May 17, 2007 (127)
7 ILLUMINA ss70458805 May 23, 2008 (130)
8 ILLUMINA ss70979345 May 17, 2007 (127)
9 ILLUMINA ss75907873 Dec 07, 2007 (129)
10 EXOME_CHIP ss491581347 May 04, 2012 (137)
11 ILLUMINA ss783467111 Jul 19, 2016 (147)
12 HAMMER_LAB ss1397805406 Oct 12, 2018 (152)
13 EVA_MGP ss1711594623 Jul 19, 2016 (147)
14 ILLUMINA ss1958161204 Jul 19, 2016 (147)
15 ILLUMINA ss3022981278 Oct 12, 2018 (152)
16 ILLUMINA ss3640947742 Oct 12, 2018 (152)
17 ILLUMINA ss3645007107 Oct 12, 2018 (152)
18 ILLUMINA ss3653538791 Oct 12, 2018 (152)
19 ILLUMINA ss3726656082 Jul 14, 2019 (153)
20 ILLUMINA ss3745540322 Jul 14, 2019 (153)
21 HGDP ss3847966392 Apr 27, 2020 (154)
22 SGDP_PRJ ss3892818874 Apr 27, 2020 (154)
23 EVA ss3984773694 Apr 27, 2021 (155)
24 TOMMO_GENOMICS ss5236850464 Apr 27, 2021 (155)
25 Genome-wide autozygosity in Daghestan NC_001807.4 - 3548 Apr 27, 2020 (154)
26 HGDP-CEPH-db Supplement 1 NC_001807.4 - 3548 Apr 27, 2020 (154)
27 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 3547 Apr 27, 2020 (154)
28 CNV burdens in cranial meningiomas NC_012920.1 - 3547 Apr 27, 2021 (155)
29 SGDP_PRJ NC_012920.1 - 3547 Apr 27, 2020 (154)
30 8.3KJPN NC_012920.1 - 3547 Apr 27, 2021 (155)
31 ALFA NC_012920.1 - 3547 Apr 27, 2021 (155)
32 ClinVar RCV000853675.1 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
542976, 644284, ss35463095, ss1397805406, ss3847966392 NC_001807.4:3547:A:G NC_012920.1:3546:A:G (self)
RCV000853675.1, 710383, 312394, 44835854, 94819771, 4890608263, ss37044375, ss66863445, ss66931980, ss68074753, ss69268935, ss70458805, ss70979345, ss75907873, ss491581347, ss783467111, ss1711594623, ss1958161204, ss3022981278, ss3640947742, ss3645007107, ss3653538791, ss3726656082, ss3745540322, ss3892818874, ss3984773694, ss5236850464 NC_012920.1:3546:A:G NC_012920.1:3546: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 rs28358586

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