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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.

rs531187028

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:193637943 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000008 (2/264690, TOPMED)
C=0.000020 (5/250862, GnomAD_exome)
C=0.000007 (1/140268, GnomAD) (+ 5 more)
C=0.000034 (4/117600, ExAC)
C=0.00004 (1/28258, 14KJPN)
C=0.00000 (0/11862, ALFA)
C=0.0003 (2/6404, 1000G_30x)
C=0.0004 (2/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
OPA1 : 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 11862 T=1.00000 C=0.00000
European Sub 7618 T=1.0000 C=0.0000
African Sub 2816 T=1.0000 C=0.0000
African Others Sub 108 T=1.000 C=0.000
African American Sub 2708 T=1.0000 C=0.0000
Asian Sub 108 T=1.000 C=0.000
East Asian Sub 84 T=1.00 C=0.00
Other Asian Sub 24 T=1.00 C=0.00
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=1.000 C=0.000
South Asian Sub 94 T=1.00 C=0.00
Other Sub 470 T=1.000 C=0.000


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 T=0.999992 C=0.000008
gnomAD - Exomes Global Study-wide 250862 T=0.999980 C=0.000020
gnomAD - Exomes European Sub 135012 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 48900 T=0.99990 C=0.00010
gnomAD - Exomes American Sub 34528 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16238 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10064 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6120 T=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140268 T=0.999993 C=0.000007
gnomAD - Genomes European Sub 75948 T=1.00000 C=0.00000
gnomAD - Genomes African Sub 42060 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13654 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 T=0.9997 C=0.0003
gnomAD - Genomes Other Sub 2152 T=1.0000 C=0.0000
ExAC Global Study-wide 117600 T=0.999966 C=0.000034
ExAC Europe Sub 71572 T=1.00000 C=0.00000
ExAC Asian Sub 23978 T=0.99983 C=0.00017
ExAC American Sub 11086 T=1.00000 C=0.00000
ExAC African Sub 10102 T=1.00000 C=0.00000
ExAC Other Sub 862 T=1.000 C=0.000
14KJPN JAPANESE Study-wide 28258 T=0.99996 C=0.00004
Allele Frequency Aggregator Total Global 11862 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 7618 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2816 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 470 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 108 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 94 T=1.00 C=0.00
1000Genomes_30x Global Study-wide 6404 T=0.9997 C=0.0003
1000Genomes_30x African Sub 1786 T=1.0000 C=0.0000
1000Genomes_30x Europe Sub 1266 T=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 T=0.9983 C=0.0017
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=1.000 C=0.000
1000Genomes Global Study-wide 5008 T=0.9996 C=0.0004
1000Genomes African Sub 1322 T=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=0.998 C=0.002
1000Genomes American Sub 694 T=1.000 C=0.000
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 3 NC_000003.12:g.193637943T>C
GRCh37.p13 chr 3 NC_000003.11:g.193355732T>C
OPA1 RefSeqGene (LRG_337) NG_011605.1:g.49800T>C
Gene: OPA1, OPA1 mitochondrial dynamin like GTPase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
OPA1 transcript variant 9 NM_001354663.2:c.502-9T>C N/A Intron Variant
OPA1 transcript variant 10 NM_001354664.2:c.499-9T>C N/A Intron Variant
OPA1 transcript variant 1 NM_015560.3:c.871-9T>C N/A Intron Variant
OPA1 transcript variant 2 NM_130831.3:c.763-9T>C N/A Intron Variant
OPA1 transcript variant 3 NM_130832.3:c.817-9T>C N/A Intron Variant
OPA1 transcript variant 4 NM_130833.3:c.874-9T>C N/A Intron Variant
OPA1 transcript variant 5 NM_130834.3:c.925-9T>C N/A Intron Variant
OPA1 transcript variant 6 NM_130835.3:c.928-9T>C N/A Intron Variant
OPA1 transcript variant 7 NM_130836.3:c.982-9T>C N/A Intron Variant
OPA1 transcript variant 8 NM_130837.3:c.1036-9T>C N/A Intron Variant
OPA1 transcript variant X1 XM_047448206.1:c.1036-9T>C N/A Intron Variant
OPA1 transcript variant X2 XM_047448207.1:c.982-9T>C N/A Intron Variant
OPA1 transcript variant X3 XM_047448208.1:c.925-9T>C N/A Intron Variant
OPA1 transcript variant X4 XM_047448209.1:c.874-9T>C N/A Intron Variant
OPA1 transcript variant X5 XM_047448210.1:c.871-9T>C N/A Intron Variant
OPA1 transcript variant X6 XM_047448211.1:c.763-9T>C N/A Intron Variant
OPA1 transcript variant X7 XM_047448212.1:c.664-9T>C N/A Intron Variant
OPA1 transcript variant X8 XM_047448213.1:c.1036-9T>C N/A Intron Variant
OPA1 transcript variant X9 XM_047448214.1:c.73-9T>C N/A Intron Variant
OPA1 transcript variant X10 XM_047448216.1:c.73-9T>C N/A Intron 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: C (allele ID: 290533 )
ClinVar Accession Disease Names Clinical Significance
RCV000330155.3 Autosomal dominant optic atrophy classic form Uncertain-Significance
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 T= C
GRCh38.p14 chr 3 NC_000003.12:g.193637943= NC_000003.12:g.193637943T>C
GRCh37.p13 chr 3 NC_000003.11:g.193355732= NC_000003.11:g.193355732T>C
OPA1 RefSeqGene (LRG_337) NG_011605.1:g.49800= NG_011605.1:g.49800T>C
OPA1 transcript variant 9 NM_001354663.2:c.502-9= NM_001354663.2:c.502-9T>C
OPA1 transcript variant 10 NM_001354664.2:c.499-9= NM_001354664.2:c.499-9T>C
OPA1 transcript variant 1 NM_015560.2:c.871-9= NM_015560.2:c.871-9T>C
OPA1 transcript variant 1 NM_015560.3:c.871-9= NM_015560.3:c.871-9T>C
OPA1 transcript variant 2 NM_130831.2:c.763-9= NM_130831.2:c.763-9T>C
OPA1 transcript variant 2 NM_130831.3:c.763-9= NM_130831.3:c.763-9T>C
OPA1 transcript variant 3 NM_130832.2:c.817-9= NM_130832.2:c.817-9T>C
OPA1 transcript variant 3 NM_130832.3:c.817-9= NM_130832.3:c.817-9T>C
OPA1 transcript variant 4 NM_130833.2:c.874-9= NM_130833.2:c.874-9T>C
OPA1 transcript variant 4 NM_130833.3:c.874-9= NM_130833.3:c.874-9T>C
OPA1 transcript variant 5 NM_130834.2:c.925-9= NM_130834.2:c.925-9T>C
OPA1 transcript variant 5 NM_130834.3:c.925-9= NM_130834.3:c.925-9T>C
OPA1 transcript variant 6 NM_130835.2:c.928-9= NM_130835.2:c.928-9T>C
OPA1 transcript variant 6 NM_130835.3:c.928-9= NM_130835.3:c.928-9T>C
OPA1 transcript variant 7 NM_130836.2:c.982-9= NM_130836.2:c.982-9T>C
OPA1 transcript variant 7 NM_130836.3:c.982-9= NM_130836.3:c.982-9T>C
OPA1 transcript variant 8 NM_130837.2:c.1036-9= NM_130837.2:c.1036-9T>C
OPA1 transcript variant 8 NM_130837.3:c.1036-9= NM_130837.3:c.1036-9T>C
OPA1 transcript variant X1 XM_005247500.1:c.1036-9= XM_005247500.1:c.1036-9T>C
OPA1 transcript variant X2 XM_005247501.1:c.982-9= XM_005247501.1:c.982-9T>C
OPA1 transcript variant X3 XM_005247502.1:c.925-9= XM_005247502.1:c.925-9T>C
OPA1 transcript variant X4 XM_005247503.1:c.874-9= XM_005247503.1:c.874-9T>C
OPA1 transcript variant X5 XM_005247504.1:c.871-9= XM_005247504.1:c.871-9T>C
OPA1 transcript variant X1 XM_047448206.1:c.1036-9= XM_047448206.1:c.1036-9T>C
OPA1 transcript variant X2 XM_047448207.1:c.982-9= XM_047448207.1:c.982-9T>C
OPA1 transcript variant X3 XM_047448208.1:c.925-9= XM_047448208.1:c.925-9T>C
OPA1 transcript variant X4 XM_047448209.1:c.874-9= XM_047448209.1:c.874-9T>C
OPA1 transcript variant X5 XM_047448210.1:c.871-9= XM_047448210.1:c.871-9T>C
OPA1 transcript variant X6 XM_047448211.1:c.763-9= XM_047448211.1:c.763-9T>C
OPA1 transcript variant X7 XM_047448212.1:c.664-9= XM_047448212.1:c.664-9T>C
OPA1 transcript variant X8 XM_047448213.1:c.1036-9= XM_047448213.1:c.1036-9T>C
OPA1 transcript variant X9 XM_047448214.1:c.73-9= XM_047448214.1:c.73-9T>C
OPA1 transcript variant X10 XM_047448216.1:c.73-9= XM_047448216.1:c.73-9T>C
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#.

10 SubSNP, 8 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1307889514 Aug 21, 2014 (142)
2 EVA_EXAC ss1687344527 Apr 01, 2015 (144)
3 GNOMAD ss2734279267 Nov 08, 2017 (151)
4 GNOMAD ss4088378893 Apr 26, 2021 (155)
5 TOPMED ss4598653622 Apr 26, 2021 (155)
6 1000G_HIGH_COVERAGE ss5257547021 Oct 13, 2022 (156)
7 EVA ss5346043611 Oct 13, 2022 (156)
8 1000G_HIGH_COVERAGE ss5537774864 Oct 13, 2022 (156)
9 TOMMO_GENOMICS ss5696985657 Oct 13, 2022 (156)
10 EVA ss5872743998 Oct 13, 2022 (156)
11 1000Genomes NC_000003.11 - 193355732 Oct 12, 2018 (152)
12 1000Genomes_30x NC_000003.12 - 193637943 Oct 13, 2022 (156)
13 ExAC NC_000003.11 - 193355732 Oct 12, 2018 (152)
14 gnomAD - Genomes NC_000003.12 - 193637943 Apr 26, 2021 (155)
15 gnomAD - Exomes NC_000003.11 - 193355732 Jul 13, 2019 (153)
16 14KJPN NC_000003.12 - 193637943 Oct 13, 2022 (156)
17 TopMed NC_000003.12 - 193637943 Apr 26, 2021 (155)
18 ALFA NC_000003.12 - 193637943 Apr 26, 2021 (155)
19 ClinVar RCV000330155.3 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
19220004, 7295618, 3375185, ss1307889514, ss1687344527, ss2734279267, ss5346043611 NC_000003.11:193355731:T:C NC_000003.12:193637942:T:C (self)
RCV000330155.3, 25300799, 136457348, 30822761, 436031177, 1003337858, ss4088378893, ss4598653622, ss5257547021, ss5537774864, ss5696985657, ss5872743998 NC_000003.12:193637942:T:C NC_000003.12:193637942:T:C (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 rs531187028

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