Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs3088053

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:11812 (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>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.06417 (1654/25776, ALFA)
G=0.0214 (44/2056, HGDP_Stanford)
G=0.034 (18/534, MGP) (+ 1 more)
C=0.3 (2/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MT-ND4 : Synonymous Variant
MT-ND5 : 2KB Upstream Variant
Publications
1 citation
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-ND5, mitochondrially encoded NADH dehydrogenase 5 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.11812A>C L [CTA] > L [CTC] Coding Sequence Variant
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu351= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.11812A>C N/A N/A
MT NC_012920.1:m.11812A>G L [CTA] > L [CTG] Coding Sequence Variant
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu351= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.11812A>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.11812A>C L [CTA] > L [CTC] Coding Sequence Variant
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu351= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.11812A>C N/A N/A
MT NC_012920.1:m.11812A>G L [CTA] > L [CTG] Coding Sequence Variant
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu351= L (Leu) > L (Leu) Synonymous Variant
MT NC_012920.1:m.11812A>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.

Not Reported in ClinVar

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 25776 A=0.93583 G=0.06417
European Sub 22106 A=0.93124 G=0.06876
African Sub 1018 A=0.9862 G=0.0138
African Others Sub 8 A=1.0 G=0.0
African American Sub 1010 A=0.9861 G=0.0139
Asian Sub 98 A=0.98 G=0.02
East Asian Sub 68 A=1.00 G=0.00
Other Asian Sub 30 A=0.93 G=0.07
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 2554 A=0.9538 G=0.0462


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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
HGDP-CEPH-db Supplement 1 Global Study-wide 2056 A=0.9786 G=0.0214
HGDP-CEPH-db Supplement 1 Est_Asia Sub 460 A=0.996 G=0.004
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 408 A=0.980 G=0.020
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.966 G=0.034
HGDP-CEPH-db Supplement 1 Europe Sub 316 A=0.930 G=0.070
HGDP-CEPH-db Supplement 1 Africa Sub 240 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 212 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 70 A=1.00 G=0.00
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.966 G=0.034
SGDP_PRJ Global Study-wide 6 A=0.0 C=0.3, G=0.7
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= C G
MT NC_012920.1:m.11812= NC_012920.1:m.11812A>C NC_012920.1:m.11812A>G
NADH dehydrogenase subunit 4 YP_003024035.1:p.Leu351= YP_003024035.1:p.Leu351= YP_003024035.1:p.Leu351=
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#.

19 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1421099 Mar 15, 2016 (147)
2 CGAP-GAI ss4322282 Mar 15, 2016 (147)
3 SSAHASNP ss35098638 Oct 12, 2018 (152)
4 ILLUMINA ss66863426 Mar 15, 2016 (147)
5 ILLUMINA ss66931942 Mar 15, 2016 (147)
6 ILLUMINA ss68074734 Mar 15, 2016 (147)
7 ILLUMINA ss70458788 Mar 15, 2016 (147)
8 ILLUMINA ss70979328 Mar 15, 2016 (147)
9 ILLUMINA ss75903592 Mar 15, 2016 (147)
10 ILLUMINA ss410884041 Sep 27, 2011 (147)
11 EVA_MGP ss1711594921 Jul 19, 2016 (147)
12 ILLUMINA ss2711176123 Oct 12, 2018 (152)
13 AFFY ss2986125593 Oct 12, 2018 (152)
14 SWEGEN ss3020999270 Oct 12, 2018 (152)
15 ILLUMINA ss3022981684 Oct 12, 2018 (152)
16 ILLUMINA ss3653539087 Oct 12, 2018 (152)
17 ILLUMINA ss3726656392 Jul 14, 2019 (153)
18 HGDP ss3847966475 Apr 27, 2020 (154)
19 SGDP_PRJ ss3892819679 Apr 27, 2020 (154)
20 HGDP-CEPH-db Supplement 1 NC_001807.4 - 11813 Apr 27, 2020 (154)
21 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 11812 Apr 27, 2020 (154)
22 SGDP_PRJ NC_012920.1 - 11812 Apr 27, 2020 (154)
23 ALFA NC_012920.1 - 11812 Apr 26, 2021 (155)
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)
rs3899215 Dec 16, 2002 (110)
rs4133758 Mar 31, 2003 (113)
rs16822406 Mar 11, 2006 (126)
rs41544217 May 24, 2008 (130)
rs193302942 Feb 12, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
44836659, ss3892819679 NC_012920.1:11811:A:C NC_012920.1:11811:A:C (self)
644367, ss35098638, ss3847966475 NC_001807.4:11812:A:G NC_012920.1:11811:A:G (self)
710681, 44836659, 14266618991, ss1421099, ss4322282, ss66863426, ss66931942, ss68074734, ss70458788, ss70979328, ss75903592, ss410884041, ss1711594921, ss2711176123, ss2986125593, ss3020999270, ss3022981684, ss3653539087, ss3726656392, ss3892819679 NC_012920.1:11811:A:G NC_012920.1:11811: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.

1 citation for rs3088053
PMID Title Author Year Journal
22723804 Mitochondrial mutations and polymorphisms in psychiatric disorders. Sequeira A et al. 2012 Frontiers in genetics
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