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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.

rs542311224

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:45550398-45550403 (GRCh38.p14) 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
dupGCT
Variation Type
Indel Insertion and Deletion
Frequency
(GCT)2=0.298912 (79119/264690, TOPMED)
(GCT)2=0.303804 (42388/139524, GnomAD)
(GCT)2=0.18092 (5112/28256, 14KJPN) (+ 8 more)
(GCT)2=0.33245 (6157/18520, ALFA)
(GCT)2=0.17812 (2985/16758, 8.3KJPN)
(GCT)2=0.2394 (1199/5008, 1000G)
(GCT)2=0.3395 (1521/4480, Estonian)
(GCT)2=0.1594 (292/1832, Korea1K)
(GCT)2=0.357 (356/998, GoNL)
(GCT)2=0.320 (192/600, NorthernSweden)
(GCT)2=0.23 (9/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
OPA3 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18520 GCTGCT=0.33245 GCTGCTGCT=0.66755
European Sub 14152 GCTGCT=0.35988 GCTGCTGCT=0.64012
African Sub 2898 GCTGCT=0.2495 GCTGCTGCT=0.7505
African Others Sub 114 GCTGCT=0.263 GCTGCTGCT=0.737
African American Sub 2784 GCTGCT=0.2489 GCTGCTGCT=0.7511
Asian Sub 112 GCTGCT=0.098 GCTGCTGCT=0.902
East Asian Sub 86 GCTGCT=0.12 GCTGCTGCT=0.88
Other Asian Sub 26 GCTGCT=0.04 GCTGCTGCT=0.96
Latin American 1 Sub 146 GCTGCT=0.274 GCTGCTGCT=0.726
Latin American 2 Sub 610 GCTGCT=0.211 GCTGCTGCT=0.789
South Asian Sub 98 GCTGCT=0.32 GCTGCTGCT=0.68
Other Sub 504 GCTGCT=0.258 GCTGCTGCT=0.742


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
TopMed Global Study-wide 264690 -

No frequency provided

dupGCT=0.701088
gnomAD - Genomes Global Study-wide 139524 -

No frequency provided

dupGCT=0.696196
gnomAD - Genomes European Sub 75626 -

No frequency provided

dupGCT=0.65636
gnomAD - Genomes African Sub 41784 -

No frequency provided

dupGCT=0.74426
gnomAD - Genomes American Sub 13554 -

No frequency provided

dupGCT=0.75365
gnomAD - Genomes Ashkenazi Jewish Sub 3312 -

No frequency provided

dupGCT=0.5960
gnomAD - Genomes East Asian Sub 3110 -

No frequency provided

dupGCT=0.8691
gnomAD - Genomes Other Sub 2138 -

No frequency provided

dupGCT=0.7053
14KJPN JAPANESE Study-wide 28256 -

No frequency provided

dupGCT=0.81908
Allele Frequency Aggregator Total Global 18520 (GCT)2=0.33245 dupGCT=0.66755
Allele Frequency Aggregator European Sub 14152 (GCT)2=0.35988 dupGCT=0.64012
Allele Frequency Aggregator African Sub 2898 (GCT)2=0.2495 dupGCT=0.7505
Allele Frequency Aggregator Latin American 2 Sub 610 (GCT)2=0.211 dupGCT=0.789
Allele Frequency Aggregator Other Sub 504 (GCT)2=0.258 dupGCT=0.742
Allele Frequency Aggregator Latin American 1 Sub 146 (GCT)2=0.274 dupGCT=0.726
Allele Frequency Aggregator Asian Sub 112 (GCT)2=0.098 dupGCT=0.902
Allele Frequency Aggregator South Asian Sub 98 (GCT)2=0.32 dupGCT=0.68
8.3KJPN JAPANESE Study-wide 16758 -

No frequency provided

dupGCT=0.82188
1000Genomes Global Study-wide 5008 -

No frequency provided

dupGCT=0.7574
1000Genomes African Sub 1322 -

No frequency provided

dupGCT=0.7534
1000Genomes East Asian Sub 1008 -

No frequency provided

dupGCT=0.8849
1000Genomes Europe Sub 1006 -

No frequency provided

dupGCT=0.6650
1000Genomes South Asian Sub 978 -

No frequency provided

dupGCT=0.699
1000Genomes American Sub 694 -

No frequency provided

dupGCT=0.795
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

dupGCT=0.6605
Korean Genome Project KOREAN Study-wide 1832 -

No frequency provided

dupGCT=0.8406
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 -

No frequency provided

dupGCT=0.643
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupGCT=0.680
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupGCT=0.78
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.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 19 NC_000019.10:g.45550398GCT[3]
GRCh37.p13 chr 19 NC_000019.9:g.46053656GCT[3]
OPA3 RefSeqGene NG_013332.1:g.39462AGC[3]
Gene: OPA3, outer mitochondrial membrane lipid metabolism regulator OPA3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
OPA3 transcript variant 1 NM_001017989.3:c.143-2094…

NM_001017989.3:c.143-20947AGC[3]

N/A Intron Variant
OPA3 transcript variant 2 NM_025136.4:c.*3111_*3116= N/A 3 Prime UTR Variant
OPA3 transcript variant X1 XM_006723403.5:c.*3111_*3…

XM_006723403.5:c.*3111_*3116=

N/A 3 Prime UTR Variant
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: dupGCT (allele ID: 333881 )
ClinVar Accession Disease Names Clinical Significance
RCV000273210.3 3-Methylglutaconic aciduria type 3 Benign
RCV000377006.3 Optic Atrophy, Dominant Benign
RCV001690091.1 not provided Benign
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 (GCT)2= dupGCT
GRCh38.p14 chr 19 NC_000019.10:g.45550398_45550403= NC_000019.10:g.45550398GCT[3]
GRCh37.p13 chr 19 NC_000019.9:g.46053656_46053661= NC_000019.9:g.46053656GCT[3]
OPA3 RefSeqGene NG_013332.1:g.39462_39467= NG_013332.1:g.39462AGC[3]
OPA3 transcript variant 2 NM_025136.4:c.*3111_*3116= NM_025136.4:c.*3111AGC[3]
OPA3 transcript variant 2 NM_025136.3:c.*3111_*3116= NM_025136.3:c.*3111AGC[3]
OPA3 transcript variant X1 XM_006723403.5:c.*3111_*3116= XM_006723403.5:c.*3111AGC[3]
OPA3 transcript variant X1 XM_006723403.4:c.*3111_*3116= XM_006723403.4:c.*3111AGC[3]
OPA3 transcript variant X1 XM_006723403.3:c.*3111_*3116= XM_006723403.3:c.*3111AGC[3]
OPA3 transcript variant 1 NM_001017989.2:c.143-20942= NM_001017989.2:c.143-20947AGC[3]
OPA3 transcript variant 1 NM_001017989.3:c.143-20942= NM_001017989.3:c.143-20947AGC[3]
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#.

54 SubSNP, 11 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ABI ss40991000 Mar 15, 2006 (136)
2 BCMHGSC_JDW ss103848917 Dec 06, 2013 (136)
3 GMI ss155774737 Dec 01, 2009 (136)
4 BL ss256207276 May 09, 2011 (136)
5 GMI ss289390659 May 04, 2012 (136)
6 1000GENOMES ss327908581 May 09, 2011 (136)
7 1000GENOMES ss328035588 May 09, 2011 (136)
8 1000GENOMES ss328278574 May 09, 2011 (136)
9 LUNTER ss552629524 Apr 25, 2013 (136)
10 LUNTER ss553017337 Apr 25, 2013 (136)
11 LUNTER ss553665179 Apr 25, 2013 (136)
12 TISHKOFF ss565722704 Apr 25, 2013 (136)
13 SSMP ss664446663 Apr 01, 2015 (144)
14 EVA-GONL ss994343966 Aug 21, 2014 (142)
15 1000GENOMES ss1378196836 Aug 21, 2014 (142)
16 DDI ss1536894406 Apr 01, 2015 (144)
17 EVA_GENOME_DK ss1575291435 Apr 01, 2015 (144)
18 EVA_DECODE ss1698399087 Apr 01, 2015 (144)
19 HAMMER_LAB ss1809328061 Sep 08, 2015 (146)
20 GENOMED ss1968651348 Jul 19, 2016 (147)
21 JJLAB ss2031409324 Sep 14, 2016 (149)
22 CLINVAR ss2137088067 Dec 21, 2016 (149)
23 SYSTEMSBIOZJU ss2629345589 Nov 08, 2017 (151)
24 SWEGEN ss3017549478 Nov 08, 2017 (151)
25 MCHAISSO ss3063917895 Nov 08, 2017 (151)
26 MCHAISSO ss3064766157 Nov 08, 2017 (151)
27 MCHAISSO ss3065715813 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3645523147 Oct 12, 2018 (152)
29 EGCUT_WGS ss3684294518 Jul 13, 2019 (153)
30 EVA_DECODE ss3702855973 Jul 13, 2019 (153)
31 ACPOP ss3743076714 Jul 13, 2019 (153)
32 PACBIO ss3788542821 Jul 13, 2019 (153)
33 PACBIO ss3793450755 Jul 13, 2019 (153)
34 PACBIO ss3798337648 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3821365666 Jul 13, 2019 (153)
36 EVA ss3835483605 Apr 27, 2020 (154)
37 EVA ss3841364533 Apr 27, 2020 (154)
38 EVA ss3846870614 Apr 27, 2020 (154)
39 KOGIC ss3981449181 Apr 27, 2020 (154)
40 FSA-LAB ss3984157231 Apr 26, 2021 (155)
41 FSA-LAB ss3984157232 Apr 26, 2021 (155)
42 EVA ss3986081274 Apr 26, 2021 (155)
43 GNOMAD ss4332030330 Apr 26, 2021 (155)
44 TOPMED ss5076336739 Apr 26, 2021 (155)
45 TOMMO_GENOMICS ss5227975361 Apr 26, 2021 (155)
46 1000G_HIGH_COVERAGE ss5307414691 Oct 13, 2022 (156)
47 HUGCELL_USP ss5499907771 Oct 13, 2022 (156)
48 SANFORD_IMAGENETICS ss5662485496 Oct 13, 2022 (156)
49 TOMMO_GENOMICS ss5786678763 Oct 13, 2022 (156)
50 EVA ss5800073563 Oct 13, 2022 (156)
51 YY_MCH ss5817641123 Oct 13, 2022 (156)
52 EVA ss5840613497 Oct 13, 2022 (156)
53 EVA ss5852305810 Oct 13, 2022 (156)
54 EVA ss5981057917 Oct 13, 2022 (156)
55 1000Genomes NC_000019.9 - 46053656 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000019.9 - 46053656 Oct 12, 2018 (152)
57 The Danish reference pan genome NC_000019.9 - 46053656 Apr 27, 2020 (154)
58 gnomAD - Genomes NC_000019.10 - 45550398 Apr 26, 2021 (155)
59 Genome of the Netherlands Release 5 NC_000019.9 - 46053656 Apr 27, 2020 (154)
60 Korean Genome Project NC_000019.10 - 45550398 Apr 27, 2020 (154)
61 Northern Sweden NC_000019.9 - 46053656 Jul 13, 2019 (153)
62 8.3KJPN NC_000019.9 - 46053656 Apr 26, 2021 (155)
63 14KJPN NC_000019.10 - 45550398 Oct 13, 2022 (156)
64 TopMed NC_000019.10 - 45550398 Apr 26, 2021 (155)
65 ALFA NC_000019.10 - 45550398 Apr 26, 2021 (155)
66 ClinVar RCV000273210.3 Oct 13, 2022 (156)
67 ClinVar RCV000377006.3 Oct 13, 2022 (156)
68 ClinVar RCV001690091.1 Oct 13, 2022 (156)
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)
rs10650481 Feb 27, 2017 (136)
rs35934096 Feb 27, 2017 (136)
rs78205570 May 15, 2013 (138)
rs141618602 Sep 17, 2011 (135)
rs398071195 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss256207276, ss289390659, ss327908581, ss328035588, ss328278574, ss552629524, ss553017337, ss553665179, ss1698399087 NC_000019.8:50745495::GCT NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
76759870, 30032766, 636442, 18934877, 16361579, 85944668, ss664446663, ss994343966, ss1378196836, ss1536894406, ss1575291435, ss1809328061, ss1968651348, ss2031409324, ss2629345589, ss3017549478, ss3684294518, ss3743076714, ss3788542821, ss3793450755, ss3798337648, ss3835483605, ss3841364533, ss3984157231, ss3986081274, ss5227975361, ss5662485496, ss5800073563, ss5840613497, ss5981057917 NC_000019.9:46053655::GCT NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
ss565722704, ss3984157232 NC_000019.9:46053661::GCT NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
541342422, 37827182, 120515867, 291882403, ss2137088067, ss3063917895, ss3064766157, ss3065715813, ss3645523147, ss3702855973, ss3821365666, ss3846870614, ss3981449181, ss4332030330, ss5076336739, ss5307414691, ss5499907771, ss5786678763, ss5817641123, ss5852305810 NC_000019.10:45550397::GCT NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
RCV000273210.3, RCV000377006.3, RCV001690091.1, 3304986649 NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
ss155774737 NT_011109.16:18321873::GCT NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
ss40991000 NT_011109.16:18321874::CTG NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(self)
ss103848917 NT_011109.16:18321879::GCT NC_000019.10:45550397:GCTGCT:GCTGC…

NC_000019.10:45550397:GCTGCT:GCTGCTGCT

(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 rs542311224

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07