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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:6253 (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
C=0.00379 (326/86122, ALFA)
C=0.0119 (100/8380, 8.3KJPN)
C=0.0376 (110/2922, KOREAN) (+ 2 more)
C=0.033 (26/792, PRJEB37584)
T=0.0 (0/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-CO1 : Missense Variant
MT-CO2 : 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-CO2, mitochondrially encoded cytochrome c oxidase II (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.6253T>C M [ATA] > T [ACA] Coding Sequence Variant
cytochrome c oxidase subunit I YP_003024028.1:p.Met117Thr M (Met) > T (Thr) Missense Variant
MT NC_012920.1:m.6253T>C N/A N/A
Gene: MT-CO1, mitochondrially encoded cytochrome c oxidase I (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.6253T>C M [ATA] > T [ACA] Coding Sequence Variant
cytochrome c oxidase subunit I YP_003024028.1:p.Met117Thr M (Met) > T (Thr) Missense Variant
MT NC_012920.1:m.6253T>C 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: C (allele ID: 681167 )
ClinVar Accession Disease Names Clinical Significance
RCV000853951.1 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 86122 T=0.99621 C=0.00379
European Sub 75202 T=0.99774 C=0.00226
African Sub 1892 T=0.9693 C=0.0307
African Others Sub 60 T=1.00 C=0.00
African American Sub 1832 T=0.9683 C=0.0317
Asian Sub 3280 T=0.9811 C=0.0189
East Asian Sub 2628 T=0.9772 C=0.0228
Other Asian Sub 652 T=0.997 C=0.003
Latin American 1 Sub 290 T=0.972 C=0.028
Latin American 2 Sub 314 T=0.987 C=0.013
South Asian Sub 176 T=1.000 C=0.000
Other Sub 4968 T=0.9952 C=0.0048


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
8.3KJPN JAPANESE Study-wide 8380 T=0.9881 C=0.0119
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9624 C=0.0376
CNV burdens in cranial meningiomas Global Study-wide 792 T=0.967 C=0.033
CNV burdens in cranial meningiomas CRM Sub 792 T=0.967 C=0.033
SGDP_PRJ Global Study-wide 4 T=0.0 C=1.0

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 T= C
MT NC_012920.1:m.6253= NC_012920.1:m.6253T>C
cytochrome c oxidase subunit I YP_003024028.1:p.Met117= YP_003024028.1:p.Met117Thr

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#.

21 SubSNP, 5 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491581379 May 04, 2012 (137)
2 ILLUMINA ss780786535 Jul 19, 2016 (147)
3 ILLUMINA ss783467126 Jul 19, 2016 (147)
4 ILLUMINA ss1752791285 Jul 19, 2016 (147)
5 ILLUMINA ss1917715419 Jul 19, 2016 (147)
6 ILLUMINA ss1945966408 Jul 19, 2016 (147)
7 ILLUMINA ss1958161251 Jul 19, 2016 (147)
8 ILLUMINA ss2634932578 Oct 12, 2018 (152)
9 ILLUMINA ss2711176068 Oct 12, 2018 (152)
10 SWEGEN ss3020998792 Oct 12, 2018 (152)
11 ILLUMINA ss3022981412 Oct 12, 2018 (152)
12 ILLUMINA ss3640947758 Oct 12, 2018 (152)
13 ILLUMINA ss3645007145 Oct 12, 2018 (152)
14 ILLUMINA ss3653538881 Oct 12, 2018 (152)
15 ILLUMINA ss3726656174 Jul 14, 2019 (153)
16 ILLUMINA ss3745540338 Jul 14, 2019 (153)
17 ILLUMINA ss3773032057 Jul 14, 2019 (153)
18 SGDP_PRJ ss3892819129 Apr 27, 2020 (154)
19 KRGDB ss3892821023 Apr 27, 2020 (154)
20 EVA ss3984773738 Apr 27, 2021 (155)
21 TOMMO_GENOMICS ss5236850975 Apr 27, 2021 (155)
22 KOREAN population from KRGDB NC_001807.4 - 6254 Apr 27, 2020 (154)
23 CNV burdens in cranial meningiomas NC_012920.1 - 6253 Apr 27, 2021 (155)
24 SGDP_PRJ NC_012920.1 - 6253 Apr 27, 2020 (154)
25 8.3KJPN NC_012920.1 - 6253 Apr 27, 2021 (155)
26 ALFA NC_012920.1 - 6253 Apr 27, 2021 (155)
27 ClinVar RCV000853951.1 Apr 27, 2020 (154)

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
50800073, ss3892821023 NC_001807.4:6253:T:C NC_012920.1:6252:T:C (self)
RCV000853951.1, 312439, 44836109, 94820282, 9903371624, ss491581379, ss780786535, ss783467126, ss1752791285, ss1917715419, ss1945966408, ss1958161251, ss2634932578, ss2711176068, ss3020998792, ss3022981412, ss3640947758, ss3645007145, ss3653538881, ss3726656174, ss3745540338, ss3773032057, ss3892819129, ss3984773738, ss5236850975 NC_012920.1:6252:T:C NC_012920.1:6252:T:C (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 rs200165736


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