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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.

rs193302991

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:15301 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.05984 (1008/16844, ALFA)
G=0.3394 (2844/8380, 8.3KJPN)
G=0.217 (167/768, PRJEB37584) (+ 2 more)
A=0.051 (27/534, MGP)
G=0.000 (0/224, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-CYB : Synonymous Variant
MT-ND6 : 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-ND6, mitochondrially encoded NADH dehydrogenase 6 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.15301G>A L [TTG] > L [TTA] Coding Sequence Variant
cytochrome b YP_003024038.1:p.Leu185= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.15301G>A N/A N/A
Gene: MT-CYB, mitochondrially encoded cytochrome b (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.15301G>A L [TTG] > L [TTA] Coding Sequence Variant
cytochrome b YP_003024038.1:p.Leu185= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.15301G>A 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: A (allele ID: 150283 )
ClinVar Accession Disease Names Clinical Significance
RCV000128806.1 Familial cancer of breast Likely-Pathogenic

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 16844 G=0.94016 A=0.05984
European Sub 13334 G=0.98065 A=0.01935
African Sub 1020 G=0.5578 A=0.4422
African Others Sub 8 G=0.0 A=1.0
African American Sub 1012 G=0.5623 A=0.4377
Asian Sub 100 G=0.48 A=0.52
East Asian Sub 70 G=0.46 A=0.54
Other Asian Sub 30 G=0.53 A=0.47
Latin American 1 Sub 0 G=0 A=0
Latin American 2 Sub 0 G=0 A=0
South Asian Sub 0 G=0 A=0
Other Sub 2390 G=0.8967 A=0.1033


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 G=0.3394 A=0.6606
CNV burdens in cranial meningiomas Global Study-wide 768 G=0.217 A=0.783
CNV burdens in cranial meningiomas CRM Sub 768 G=0.217 A=0.783
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.949 A=0.051
SGDP_PRJ Global Study-wide 224 G=0.000 A=1.000
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 G= A
MT NC_012920.1:m.15301= NC_012920.1:m.15301G>A
cytochrome b YP_003024038.1:p.Leu185= YP_003024038.1:p.Leu185=
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#.

35 SubSNP, 5 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35303067 May 24, 2005 (136)
2 ABI ss43551520 Mar 13, 2006 (136)
3 BROAD ss46525739 Mar 13, 2006 (136)
4 ILLUMINA ss66863436 Dec 01, 2006 (136)
5 ILLUMINA ss66931962 Dec 01, 2006 (136)
6 ILLUMINA ss68074744 Dec 12, 2006 (136)
7 ILLUMINA ss70458797 May 25, 2008 (136)
8 ILLUMINA ss70979337 May 17, 2007 (136)
9 ILLUMINA ss75901306 Dec 06, 2007 (136)
10 AFFY ss76713912 Dec 07, 2007 (136)
11 BCMHGSC_JDW ss94206257 Mar 25, 2008 (136)
12 KRIBB_YJKIM ss105106296 Feb 05, 2009 (136)
13 ILLUMINA ss152536599 Dec 01, 2009 (136)
14 ILLUMINA ss159102669 Dec 01, 2009 (136)
15 COMPLETE_GENOMICS ss163709974 Jul 04, 2010 (136)
16 ILLUMINA ss169133742 Jul 04, 2010 (136)
17 ILLUMINA ss410884090 Sep 27, 2011 (135)
18 TISHKOFF ss567118086 Apr 25, 2013 (136)
19 ILLUMINA ss832615465 Jul 14, 2019 (153)
20 MANISHAMVMBHOPAL ss1225195455 Aug 14, 2014 (141)
21 EVA_MGP ss1711595100 Jul 19, 2016 (147)
22 ILLUMINA ss1958161472 Jul 19, 2016 (147)
23 ILLUMINA ss2711176162 Oct 12, 2018 (152)
24 SWEGEN ss3020999581 Oct 12, 2018 (152)
25 ILLUMINA ss3022981922 Oct 12, 2018 (152)
26 ILLUMINA ss3625994571 Oct 12, 2018 (152)
27 ILLUMINA ss3645007316 Oct 12, 2018 (152)
28 ILLUMINA ss3653539298 Oct 12, 2018 (152)
29 ILLUMINA ss3726656603 Jul 14, 2019 (153)
30 ILLUMINA ss3744327219 Jul 14, 2019 (153)
31 HGDP ss3847966504 Apr 27, 2020 (154)
32 SGDP_PRJ ss3892820019 Apr 27, 2020 (154)
33 KRGDB ss3892822282 Apr 27, 2020 (154)
34 EVA ss3984773963 Apr 27, 2021 (155)
35 TOMMO_GENOMICS ss5236852949 Apr 27, 2021 (155)
36 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 15301 Apr 27, 2020 (154)
37 CNV burdens in cranial meningiomas NC_012920.1 - 15301 Apr 27, 2021 (155)
38 SGDP_PRJ NC_012920.1 - 15301 Apr 27, 2020 (154)
39 8.3KJPN NC_012920.1 - 15301 Apr 27, 2021 (155)
40 ALFA NC_012920.1 - 15301 Apr 27, 2021 (155)
41 ClinVar RCV000128806.1 Oct 12, 2018 (152)
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)
rs28573847 Aug 25, 2014 (136)
rs41549419 May 25, 2008 (130)
rs56121693 May 25, 2008 (130)
rs78842735 Sep 17, 2011 (135)
rs386508198 Aug 21, 2014 (142)
rs386829241 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35303067, ss94206257, ss163709974, ss832615465, ss3847966504, ss3892822282 NC_001807.4:15301:A:A NC_012920.1:15300:G:A (self)
RCV000128806.1, 710860, 312664, 44836999, 94822256, 2777024338, ss43551520, ss46525739, ss66863436, ss66931962, ss68074744, ss70458797, ss70979337, ss75901306, ss76713912, ss105106296, ss152536599, ss159102669, ss169133742, ss410884090, ss567118086, ss1225195455, ss1711595100, ss1958161472, ss2711176162, ss3020999581, ss3022981922, ss3625994571, ss3645007316, ss3653539298, ss3726656603, ss3744327219, ss3892820019, ss3984773963, ss5236852949 NC_012920.1:15300:G:A NC_012920.1:15300:G:A (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 rs193302991

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