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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.

rs190583213

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:45549097 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.003650 (966/264690, TOPMED)
A=0.003412 (478/140094, GnomAD)
A=0.00035 (10/28258, 14KJPN) (+ 8 more)
A=0.00042 (7/16760, 8.3KJPN)
A=0.00243 (35/14420, ALFA)
A=0.0033 (21/6404, 1000G_30x)
A=0.0034 (17/5008, 1000G)
A=0.0008 (3/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0017 (5/2922, KOREAN)
A=0.0027 (5/1832, Korea1K)
Clinical Significance
Not 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 14420 G=0.99757 A=0.00243
European Sub 9824 G=0.9995 A=0.0005
African Sub 2946 G=0.9922 A=0.0078
African Others Sub 114 G=0.991 A=0.009
African American Sub 2832 G=0.9922 A=0.0078
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.993 A=0.007
Latin American 2 Sub 610 G=0.998 A=0.002
South Asian Sub 98 G=1.00 A=0.00
Other Sub 684 G=0.993 A=0.007


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 G=0.996350 A=0.003650
gnomAD - Genomes Global Study-wide 140094 G=0.996588 A=0.003412
gnomAD - Genomes European Sub 75884 G=0.99953 A=0.00047
gnomAD - Genomes African Sub 41968 G=0.99030 A=0.00970
gnomAD - Genomes American Sub 13634 G=0.99795 A=0.00205
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2152 G=0.9972 A=0.0028
14KJPN JAPANESE Study-wide 28258 G=0.99965 A=0.00035
8.3KJPN JAPANESE Study-wide 16760 G=0.99958 A=0.00042
Allele Frequency Aggregator Total Global 14420 G=0.99757 A=0.00243
Allele Frequency Aggregator European Sub 9824 G=0.9995 A=0.0005
Allele Frequency Aggregator African Sub 2946 G=0.9922 A=0.0078
Allele Frequency Aggregator Other Sub 684 G=0.993 A=0.007
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.998 A=0.002
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.993 A=0.007
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9967 A=0.0033
1000Genomes_30x African Sub 1786 G=0.9899 A=0.0101
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9983 A=0.0017
1000Genomes_30x American Sub 980 G=0.999 A=0.001
1000Genomes Global Study-wide 5008 G=0.9966 A=0.0034
1000Genomes African Sub 1322 G=0.9887 A=0.0113
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9992 A=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 A=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9983 A=0.0017
Korean Genome Project KOREAN Study-wide 1832 G=0.9973 A=0.0027
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.45549097G>A
GRCh37.p13 chr 19 NC_000019.9:g.46052355G>A
OPA3 RefSeqGene NG_013332.1:g.40768C>T
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.143-1964…

NM_001017989.3:c.143-19641C>T

N/A Intron Variant
OPA3 transcript variant 2 NM_025136.4:c.*4417= N/A 3 Prime UTR Variant
OPA3 transcript variant X1 XM_006723403.5:c.*4417= 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.

Not Reported in ClinVar
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 G= A
GRCh38.p14 chr 19 NC_000019.10:g.45549097= NC_000019.10:g.45549097G>A
GRCh37.p13 chr 19 NC_000019.9:g.46052355= NC_000019.9:g.46052355G>A
OPA3 RefSeqGene NG_013332.1:g.40768= NG_013332.1:g.40768C>T
OPA3 transcript variant 2 NM_025136.4:c.*4417= NM_025136.4:c.*4417C>T
OPA3 transcript variant 2 NM_025136.3:c.*4417= NM_025136.3:c.*4417C>T
OPA3 transcript variant X1 XM_006723403.5:c.*4417= XM_006723403.5:c.*4417C>T
OPA3 transcript variant X1 XM_006723403.4:c.*4417= XM_006723403.4:c.*4417C>T
OPA3 transcript variant X1 XM_006723403.3:c.*4417= XM_006723403.3:c.*4417C>T
OPA3 transcript variant 1 NM_001017989.2:c.143-19641= NM_001017989.2:c.143-19641C>T
OPA3 transcript variant 1 NM_001017989.3:c.143-19641= NM_001017989.3:c.143-19641C>T
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, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss465619288 Sep 17, 2011 (135)
2 1000GENOMES ss1363346450 Aug 21, 2014 (142)
3 EVA_UK10K_ALSPAC ss1638052755 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1681046788 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2226053710 Dec 20, 2016 (150)
6 GNOMAD ss2963389659 Nov 08, 2017 (151)
7 EVA ss3756117376 Jul 13, 2019 (153)
8 KRGDB ss3938446013 Apr 27, 2020 (154)
9 KOGIC ss3981449158 Apr 27, 2020 (154)
10 TOPMED ss5076336427 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5227975319 Apr 26, 2021 (155)
12 1000G_HIGH_COVERAGE ss5307414653 Oct 13, 2022 (156)
13 EVA ss5435120246 Oct 13, 2022 (156)
14 HUGCELL_USP ss5499907738 Oct 13, 2022 (156)
15 1000G_HIGH_COVERAGE ss5613218013 Oct 13, 2022 (156)
16 SANFORD_IMAGENETICS ss5662485474 Oct 13, 2022 (156)
17 TOMMO_GENOMICS ss5786678707 Oct 13, 2022 (156)
18 EVA ss5928276348 Oct 13, 2022 (156)
19 EVA ss5953894938 Oct 13, 2022 (156)
20 1000Genomes NC_000019.9 - 46052355 Oct 12, 2018 (152)
21 1000Genomes_30x NC_000019.10 - 45549097 Oct 13, 2022 (156)
22 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 46052355 Oct 12, 2018 (152)
23 gnomAD - Genomes NC_000019.10 - 45549097 Apr 26, 2021 (155)
24 KOREAN population from KRGDB NC_000019.9 - 46052355 Apr 27, 2020 (154)
25 Korean Genome Project NC_000019.10 - 45549097 Apr 27, 2020 (154)
26 8.3KJPN NC_000019.9 - 46052355 Apr 26, 2021 (155)
27 14KJPN NC_000019.10 - 45549097 Oct 13, 2022 (156)
28 TopMed NC_000019.10 - 45549097 Apr 26, 2021 (155)
29 UK 10K study - Twins NC_000019.9 - 46052355 Oct 12, 2018 (152)
30 ALFA NC_000019.10 - 45549097 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
76759828, 42504086, 45623407, 85944626, 42504086, ss465619288, ss1363346450, ss1638052755, ss1681046788, ss2963389659, ss3756117376, ss3938446013, ss5227975319, ss5435120246, ss5662485474, ss5953894938 NC_000019.9:46052354:G:A NC_000019.10:45549096:G:A (self)
100743948, 541342151, 37827159, 120515811, 291882091, 6822821214, ss2226053710, ss3981449158, ss5076336427, ss5307414653, ss5499907738, ss5613218013, ss5786678707, ss5928276348 NC_000019.10:45549096:G:A NC_000019.10:45549096:G:A (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 rs190583213

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