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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.

rs2853506

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:15218 (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=0.037665 (5901/156670, ALFA)
G=0.0069 (58/8380, 8.3KJPN)
G=0.0205 (60/2922, KOREAN) (+ 4 more)
G=0.0138 (28/2032, HGDP_Stanford)
G=0.024 (18/762, PRJEB37584)
G=0.026 (14/534, MGP)
A=0.0 (0/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-CYB : Missense 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.15218A>G T [ACA] > A [GCA] Coding Sequence Variant
cytochrome b YP_003024038.1:p.Thr158Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.15218A>G 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.15218A>G T [ACA] > A [GCA] Coding Sequence Variant
cytochrome b YP_003024038.1:p.Thr158Ala T (Thr) > A (Ala) Missense Variant
MT NC_012920.1:m.15218A>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: 680733 )
ClinVar Accession Disease Names Clinical Significance
RCV000855243.1 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 156670 A=0.962335 G=0.037665
European Sub 142210 A=0.961121 G=0.038879
African Sub 1550 A=0.9897 G=0.0103
African Others Sub 62 A=1.00 G=0.00
African American Sub 1488 A=0.9892 G=0.0108
Asian Sub 3200 A=0.9762 G=0.0238
East Asian Sub 2566 A=0.9704 G=0.0296
Other Asian Sub 634 A=1.000 G=0.000
Latin American 1 Sub 296 A=1.000 G=0.000
Latin American 2 Sub 338 A=0.994 G=0.006
South Asian Sub 176 A=0.989 G=0.011
Other Sub 8900 A=0.9690 G=0.0310


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=0.9931 G=0.0069
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9795 G=0.0205
HGDP-CEPH-db Supplement 1 Global Study-wide 2032 A=0.9862 G=0.0138
HGDP-CEPH-db Supplement 1 Est_Asia Sub 462 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 406 A=0.985 G=0.015
HGDP-CEPH-db Supplement 1 Middle_Est Sub 342 A=0.971 G=0.029
HGDP-CEPH-db Supplement 1 Europe Sub 312 A=0.962 G=0.038
HGDP-CEPH-db Supplement 1 Africa Sub 222 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 72 A=1.00 G=0.00
CNV burdens in cranial meningiomas Global Study-wide 762 A=0.976 G=0.024
CNV burdens in cranial meningiomas CRM Sub 762 A=0.976 G=0.024
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.974 G=0.026
SGDP_PRJ Global Study-wide 6 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.15218= NC_012920.1:m.15218A>G
cytochrome b YP_003024038.1:p.Thr158= YP_003024038.1:p.Thr158Ala
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#.

36 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4040105 Sep 28, 2001 (100)
2 ILLUMINA ss66863434 Dec 01, 2006 (127)
3 ILLUMINA ss66931958 Dec 01, 2006 (127)
4 ILLUMINA ss68074742 Dec 12, 2006 (130)
5 ILLUMINA ss70458795 May 25, 2008 (130)
6 ILLUMINA ss70979335 May 17, 2007 (127)
7 ILLUMINA ss75891447 Dec 07, 2007 (129)
8 AFFY ss76713231 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss104882240 Feb 05, 2009 (130)
10 EXOME_CHIP ss491581511 May 04, 2012 (137)
11 ILLUMINA ss780683989 Jul 19, 2016 (147)
12 ILLUMINA ss783357412 Jul 19, 2016 (147)
13 EVA_MGP ss1711595092 Jul 19, 2016 (147)
14 ILLUMINA ss1752791184 Jul 19, 2016 (147)
15 ILLUMINA ss1917715513 Jul 19, 2016 (147)
16 ILLUMINA ss1945966618 Jul 19, 2016 (147)
17 ILLUMINA ss1958161468 Jul 19, 2016 (147)
18 ILLUMINA ss2634932731 Oct 12, 2018 (152)
19 ILLUMINA ss2711176160 Oct 12, 2018 (152)
20 AFFY ss2986125625 Oct 12, 2018 (152)
21 SWEGEN ss3020999573 Oct 12, 2018 (152)
22 ILLUMINA ss3022981913 Oct 12, 2018 (152)
23 ILLUMINA ss3630385203 Oct 12, 2018 (152)
24 ILLUMINA ss3635240405 Oct 12, 2018 (152)
25 ILLUMINA ss3640947851 Oct 12, 2018 (152)
26 ILLUMINA ss3645007312 Oct 12, 2018 (152)
27 ILLUMINA ss3653539290 Oct 12, 2018 (152)
28 ILLUMINA ss3726656595 Jul 14, 2019 (153)
29 ILLUMINA ss3744596948 Jul 14, 2019 (153)
30 ILLUMINA ss3745540430 Jul 14, 2019 (153)
31 ILLUMINA ss3773032150 Jul 14, 2019 (153)
32 HGDP ss3847966501 Apr 27, 2020 (154)
33 SGDP_PRJ ss3892820005 Apr 27, 2020 (154)
34 KRGDB ss3892822262 Apr 27, 2020 (154)
35 EVA ss3984773955 Apr 27, 2021 (155)
36 TOMMO_GENOMICS ss5236852915 Apr 27, 2021 (155)
37 HGDP-CEPH-db Supplement 1 NC_001807.4 - 15219 Apr 27, 2020 (154)
38 KOREAN population from KRGDB NC_001807.4 - 15219 Apr 27, 2020 (154)
39 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 15218 Apr 27, 2020 (154)
40 CNV burdens in cranial meningiomas NC_012920.1 - 15218 Apr 27, 2021 (155)
41 SGDP_PRJ NC_012920.1 - 15218 Apr 27, 2020 (154)
42 8.3KJPN NC_012920.1 - 15218 Apr 27, 2021 (155)
43 ALFA NC_012920.1 - 15218 Apr 27, 2021 (155)
44 ClinVar RCV000855243.1 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)
rs41553214 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644393, 50801312, ss76713231, ss3847966501, ss3892822262 NC_001807.4:15218:A:G NC_012920.1:15217:A:G (self)
RCV000855243.1, 710852, 312656, 44836985, 94822222, 4890239055, ss4040105, ss66863434, ss66931958, ss68074742, ss70458795, ss70979335, ss75891447, ss104882240, ss491581511, ss780683989, ss783357412, ss1711595092, ss1752791184, ss1917715513, ss1945966618, ss1958161468, ss2634932731, ss2711176160, ss2986125625, ss3020999573, ss3022981913, ss3630385203, ss3635240405, ss3640947851, ss3645007312, ss3653539290, ss3726656595, ss3744596948, ss3745540430, ss3773032150, ss3892820005, ss3984773955, ss5236852915 NC_012920.1:15217:A:G NC_012920.1:15217: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 rs2853506

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