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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.

rs193303001

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:15924 (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=0.06365 (2535/39828, ALFA)
G=0.0122 (102/8380, 8.3KJPN)
G=0.0116 (34/2922, KOREAN) (+ 3 more)
G=0.0320 (65/2032, HGDP_Stanford)
G=0.011 (6/534, MGP)
A=0.00 (0/18, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-CYB : 500B Downstream Variant
MT-ND6 : 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-CYB, mitochondrially encoded cytochrome b (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.15924A>G N/A N/A
MT NC_012920.1:m.15924A>G N/A N/A
Gene: MT-ND6, mitochondrially encoded NADH dehydrogenase 6 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.15924A>G N/A N/A
MT NC_012920.1:m.15924A>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: 677628 )
ClinVar Accession Disease Names Clinical Significance
RCV000851128.1 Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign

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 39828 A=0.93635 G=0.06365
European Sub 36380 A=0.93826 G=0.06174
African Sub 624 A=0.925 G=0.075
African Others Sub 8 A=1.0 G=0.0
African American Sub 616 A=0.924 G=0.076
Asian Sub 60 A=1.00 G=0.00
East Asian Sub 30 A=1.00 G=0.00
Other Asian Sub 30 A=1.00 G=0.00
Latin American 1 Sub 6 A=1.0 G=0.0
Latin American 2 Sub 22 A=1.00 G=0.00
South Asian Sub 0 A=0 G=0
Other Sub 2736 A=0.9115 G=0.0885


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=0.9878 G=0.0122
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9884 G=0.0116
HGDP-CEPH-db Supplement 1 Global Study-wide 2032 A=0.9680 G=0.0320
HGDP-CEPH-db Supplement 1 Est_Asia Sub 466 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 408 A=0.971 G=0.029
HGDP-CEPH-db Supplement 1 Middle_Est Sub 340 A=0.971 G=0.029
HGDP-CEPH-db Supplement 1 Europe Sub 304 A=0.964 G=0.036
HGDP-CEPH-db Supplement 1 Africa Sub 240 A=0.992 G=0.008
HGDP-CEPH-db Supplement 1 America Sub 206 A=0.854 G=0.146
HGDP-CEPH-db Supplement 1 Oceania Sub 68 A=1.00 G=0.00
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.989 G=0.011
SGDP_PRJ Global Study-wide 18 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.15924= NC_012920.1:m.15924A>G
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#.

46 SubSNP, 8 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4040109 Sep 28, 2001 (136)
2 SSAHASNP ss35177916 May 24, 2005 (136)
3 ABI ss43522101 Mar 13, 2006 (136)
4 BROAD ss46525744 Mar 13, 2006 (136)
5 ILLUMINA ss66863439 Nov 29, 2006 (136)
6 ILLUMINA ss66931968 Nov 29, 2006 (136)
7 ILLUMINA ss68074747 Dec 12, 2006 (136)
8 ILLUMINA ss70458799 May 25, 2008 (136)
9 ILLUMINA ss70979339 May 16, 2007 (136)
10 ILLUMINA ss75883265 Dec 06, 2007 (136)
11 AFFY ss76713483 Dec 06, 2007 (136)
12 KRIBB_YJKIM ss104882243 Feb 05, 2009 (136)
13 ILLUMINA ss152536610 Dec 01, 2009 (136)
14 ILLUMINA ss159102671 Dec 01, 2009 (136)
15 ILLUMINA ss169133772 Jul 04, 2010 (136)
16 ILLUMINA ss410884100 Sep 27, 2011 (135)
17 ILLUMINA ss479152854 May 04, 2012 (136)
18 ILLUMINA ss484376879 May 04, 2012 (136)
19 EXOME_CHIP ss491581540 May 04, 2012 (136)
20 ILLUMINA ss536559245 Jul 19, 2016 (136)
21 SSMP ss662653025 May 31, 2013 (136)
22 ILLUMINA ss780683990 Jul 19, 2016 (136)
23 ILLUMINA ss782634734 Oct 12, 2018 (152)
24 ILLUMINA ss783357413 Jul 19, 2016 (136)
25 ILLUMINA ss832615467 Jul 14, 2019 (153)
26 ILLUMINA ss836124382 Oct 12, 2018 (152)
27 EVA_MGP ss1711595139 Jul 19, 2016 (136)
28 ILLUMINA ss1752791210 Jul 19, 2016 (136)
29 ILLUMINA ss1917715539 Jul 19, 2016 (136)
30 ILLUMINA ss1945966649 Jul 19, 2016 (136)
31 ILLUMINA ss1958161504 Jul 19, 2016 (136)
32 ILLUMINA ss2634932753 Oct 12, 2018 (152)
33 SWEGEN ss3020999655 Oct 12, 2018 (152)
34 ILLUMINA ss3645007343 Oct 12, 2018 (152)
35 ILLUMINA ss3653539338 Oct 12, 2018 (152)
36 ILLUMINA ss3726656646 Jul 14, 2019 (153)
37 ILLUMINA ss3744596951 Jul 14, 2019 (153)
38 ILLUMINA ss3745540455 Jul 14, 2019 (153)
39 ILLUMINA ss3773032176 Jul 14, 2019 (153)
40 HGDP ss3847966511 Apr 27, 2020 (154)
41 SGDP_PRJ ss3892820097 Apr 27, 2020 (154)
42 KRGDB ss3892822392 Apr 27, 2020 (154)
43 EVA ss3984773996 Apr 27, 2021 (155)
44 EVA ss3984773997 Apr 27, 2021 (155)
45 TOMMO_GENOMICS ss5236853124 Apr 27, 2021 (155)
46 EVA ss5237630465 Apr 27, 2021 (155)
47 HGDP-CEPH-db Supplement 1 NC_001807.4 - 15925 Apr 27, 2020 (154)
48 KOREAN population from KRGDB NC_001807.4 - 15925 Apr 27, 2020 (154)
49 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 15924 Apr 27, 2020 (154)
50 CNV burdens in cranial meningiomas

Submission ignored due to conflicting rows:
Row 312697 (NC_012920.1:15923:A:G 1/792)
Row 312698 (NC_012920.1:15923:A:G 1/792)

- Apr 27, 2021 (155)
51 CNV burdens in cranial meningiomas

Submission ignored due to conflicting rows:
Row 312697 (NC_012920.1:15923:A:G 1/792)
Row 312698 (NC_012920.1:15923:A:G 1/792)

- Apr 27, 2021 (155)
52 SGDP_PRJ NC_012920.1 - 15924 Apr 27, 2020 (154)
53 8.3KJPN NC_012920.1 - 15924 Apr 27, 2021 (155)
54 ALFA NC_012920.1 - 15924 Apr 27, 2021 (155)
55 ClinVar RCV000851128.1 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)
rs2853510 Feb 27, 2017 (136)
rs77381533 Jul 15, 2010 (132)
rs113124206 Sep 17, 2011 (135)
rs200457782 Aug 21, 2014 (142)
rs386508200 Aug 21, 2014 (142)
rs386829267 Aug 21, 2014 (142)
rs387907318 Jul 01, 2015 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644403, 50801442, ss35177916, ss76713483, ss479152854, ss662653025, ss782634734, ss832615467, ss836124382, ss3847966511, ss3892822392 NC_001807.4:15924:A:G NC_012920.1:15923:A:G (self)
RCV000851128.1, 710899, 44837077, 94822431, 13455284418, ss4040109, ss43522101, ss46525744, ss66863439, ss66931968, ss68074747, ss70458799, ss70979339, ss75883265, ss104882243, ss152536610, ss159102671, ss169133772, ss410884100, ss484376879, ss491581540, ss536559245, ss780683990, ss783357413, ss1711595139, ss1752791210, ss1917715539, ss1945966649, ss1958161504, ss2634932753, ss3020999655, ss3645007343, ss3653539338, ss3726656646, ss3744596951, ss3745540455, ss3773032176, ss3892820097, ss3984773996, ss3984773997, ss5236853124, ss5237630465 NC_012920.1:15923:A:G NC_012920.1:15923: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 rs193303001
PMID Title Author Year Journal
1379415 Mitochondrial tRNA(Thr) mutations and lethal infantile mitochondrial myopathy. Brown MD et al. 1992 American journal of human genetics
1645537 Mitochondrial tRNA(thr) mutation in fatal infantile respiratory enzyme deficiency. Yoon KL et al. 1991 Biochemical and biophysical research communications
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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