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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chrMT:11467 (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.

Variation Type
SNV Single Nucleotide Variation
G=0.2586 (2324/8986, ALFA)
G=0.1162 (240/2066, HGDP_Stanford)
G=0.2089 (234/1120, Daghestan) (+ 3 more)
G=0.005 (4/792, PRJEB37584)
G=0.142 (76/534, MGP)
A=0.00 (0/62, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-ND4 : Synonymous Variant
MT-ND5 : 2KB Upstream Variant
0 citations
Genomic View
See rs on genome

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-ND5, mitochondrially encoded NADH dehydrogenase 5 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.11467A>G L [TTA] > L [TTG] Coding Sequence Variant
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu236= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.11467A>G N/A N/A
Gene: MT-ND4, mitochondrially encoded NADH dehydrogenase 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.11467A>G L [TTA] > L [TTG] Coding Sequence Variant
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu236= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.11467A>G N/A N/A

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: 513402 )
ClinVar Accession Disease Names Clinical Significance
RCV000625869.1 Mitochondrial diseases Likely-Pathogenic

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 8986 A=0.7414 G=0.2586
European Sub 6062 A=0.7189 G=0.2811
African Sub 594 A=0.825 G=0.175
African Others Sub 8 A=1.0 G=0.0
African American Sub 586 A=0.823 G=0.177
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=0.7731 G=0.2269


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").

Study Population Group Sample Size Ref Allele Alt Allele
HGDP-CEPH-db Supplement 1 Global Study-wide 2066 A=0.8838 G=0.1162
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=0.996 G=0.004
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 412 A=0.811 G=0.189
HGDP-CEPH-db Supplement 1 Middle_Est Sub 344 A=0.744 G=0.256
HGDP-CEPH-db Supplement 1 Europe Sub 312 A=0.769 G=0.231
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 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 1120 A=0.7911 G=0.2089
Genome-wide autozygosity in Daghestan Daghestan Sub 624 A=0.776 G=0.224
Genome-wide autozygosity in Daghestan Near_East Sub 142 A=0.831 G=0.169
Genome-wide autozygosity in Daghestan Central Asia Sub 114 A=0.877 G=0.123
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.722 G=0.278
Genome-wide autozygosity in Daghestan South Asian Sub 96 A=0.81 G=0.19
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.78 G=0.22
CNV burdens in cranial meningiomas Global Study-wide 792 A=0.995 G=0.005
CNV burdens in cranial meningiomas CRM Sub 792 A=0.995 G=0.005
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.858 G=0.142
SGDP_PRJ Global Study-wide 62 A=0.00 G=1.00

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.11467= NC_012920.1:m.11467A>G
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu236= YP_003024035.1:p.Leu236=

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#.

41 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1421102 Oct 08, 2002 (110)
2 TSC-CSHL ss1426311 Oct 10, 2002 (123)
3 SC_JCM ss4040092 Sep 28, 2001 (100)
4 TSC-CSHL ss5167311 Oct 08, 2002 (110)
5 TSC-CSHL ss5583707 Oct 10, 2002 (113)
6 TSC-CSHL ss5583905 Oct 10, 2002 (113)
7 SEQUENOM ss24792795 Sep 20, 2004 (124)
8 SSAHASNP ss35470232 May 24, 2005 (125)
9 BROAD ss46525719 Mar 15, 2006 (126)
10 ILLUMINA ss66863425 Dec 02, 2006 (127)
11 ILLUMINA ss66931940 Dec 02, 2006 (127)
12 ILLUMINA ss68074733 Dec 12, 2006 (127)
13 ILLUMINA ss70458787 May 26, 2008 (130)
14 ILLUMINA ss70979327 May 18, 2007 (127)
15 ILLUMINA ss75882386 Dec 07, 2007 (129)
16 AFFY ss76713243 Dec 07, 2007 (129)
17 KRIBB_YJKIM ss104882230 Feb 06, 2009 (130)
18 COMPLETE_GENOMICS ss163709841 Jul 04, 2010 (142)
19 ILLUMINA ss479152847 May 04, 2012 (142)
20 ILLUMINA ss484376864 May 04, 2012 (142)
21 ILLUMINA ss536559236 Jul 19, 2016 (147)
22 ILLUMINA ss782634727 Oct 12, 2018 (152)
23 ILLUMINA ss832615457 Jul 14, 2019 (153)
24 ILLUMINA ss836124375 Oct 12, 2018 (152)
25 HAMMER_LAB ss1397805517 Oct 12, 2018 (152)
26 EVA_MGP ss1711594910 Jul 19, 2016 (147)
27 ILLUMINA ss1958161363 Jul 19, 2016 (147)
28 AFFY ss2986125590 Oct 12, 2018 (152)
29 SWEGEN ss3020999251 Oct 12, 2018 (152)
30 ILLUMINA ss3022981669 Oct 12, 2018 (152)
31 ILLUMINA ss3022981670 Oct 12, 2018 (152)
32 ILLUMINA ss3625994534 Oct 12, 2018 (152)
33 ILLUMINA ss3645007229 Oct 12, 2018 (152)
34 ILLUMINA ss3653539074 Oct 12, 2018 (152)
35 ILLUMINA ss3653539075 Oct 12, 2018 (152)
36 ILLUMINA ss3726656381 Jul 14, 2019 (153)
37 ILLUMINA ss3744327183 Jul 14, 2019 (153)
38 HGDP ss3847966472 Apr 27, 2020 (154)
39 SGDP_PRJ ss3892819659 Apr 27, 2020 (154)
40 EVA ss3984773843 Apr 27, 2021 (155)
41 EVA ss5237630433 Apr 27, 2021 (155)
42 Genome-wide autozygosity in Daghestan NC_001807.4 - 11468 Apr 27, 2020 (154)
43 HGDP-CEPH-db Supplement 1 NC_001807.4 - 11468 Apr 27, 2020 (154)
44 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 11467 Apr 27, 2020 (154)
45 CNV burdens in cranial meningiomas NC_012920.1 - 11467 Apr 27, 2021 (155)
46 SGDP_PRJ NC_012920.1 - 11467 Apr 27, 2020 (154)
47 ALFA NC_012920.1 - 11467 Apr 27, 2021 (155)
48 ClinVar RCV000625869.1 Oct 12, 2018 (152)

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)
rs3883921 Dec 16, 2002 (110)
rs3899439 Sep 24, 2004 (123)
rs4133694 Mar 31, 2003 (113)
rs4133742 Mar 31, 2003 (113)
rs16822438 Dec 02, 2004 (124)
rs111422935 Aug 21, 2014 (142)
rs373240586 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
543085, 644364, ss1421102, ss1426311, ss4040092, ss5167311, ss5583707, ss5583905, ss24792795, ss35470232, ss46525719, ss66863425, ss66931940, ss68074733, ss70458787, ss70979327, ss75882386, ss76713243, ss163709841, ss479152847, ss782634727, ss832615457, ss836124375, ss1397805517, ss3847966472 NC_001807.4:11467:A:G NC_012920.1:11466:A:G (self)
RCV000625869.1, 710670, 312544, 44836639, 13649698798, ss104882230, ss484376864, ss536559236, ss1711594910, ss1958161363, ss2986125590, ss3020999251, ss3022981669, ss3022981670, ss3625994534, ss3645007229, ss3653539074, ss3653539075, ss3726656381, ss3744327183, ss3892819659, ss3984773843, ss5237630433 NC_012920.1:11466:A:G NC_012920.1:11466:A:G (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs2853493


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