dbSNP rs75414918: OPA1:p.Gln15Lys (chr3-193614733-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_130837.3(OPA1):c.43C>A(p.Gln15Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00414 in 1,612,714 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0031 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0043 ( 82 hom. )

Consequence

OPA1
NM_130837.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 3.42

Publications

13 publications found

Variant links:

Genes affected

OPA1 (HGNC:8140): (OPA1 mitochondrial dynamin like GTPase) The protein encoded by this gene is a nuclear-encoded mitochondrial protein with similarity to dynamin-related GTPases. The encoded protein localizes to the inner mitochondrial membrane and helps regulate mitochondrial stability and energy output. This protein also sequesters cytochrome c. Mutations in this gene have been associated with optic atrophy type 1, which is a dominantly inherited optic neuropathy resulting in progressive loss of visual acuity, leading in many cases to legal blindness. [provided by RefSeq, Aug 2017]

OPA1 Gene-Disease associations (from GenCC):

autosomal dominant optic atrophy, classic form
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics
optic atrophy
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
OPA1-related optic atrophy with or without extraocular features
Inheritance: SD Classification: DEFINITIVE Submitted by: ClinGen
Behr syndrome
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
mitochondrial DNA depletion syndrome 14 (cardioencephalomyopathic type)
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
Leigh syndrome
Inheritance: AR Classification: MODERATE Submitted by: ClinGen
autosomal dominant optic atrophy plus syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

OPA1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0065462887).

BP6

Variant 3-193614733-C-A is Benign according to our data. Variant chr3-193614733-C-A is described in ClinVar as Benign. ClinVar VariationId is 95726.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00307 (467/152260) while in subpopulation SAS AF = 0.0168 (81/4820). AF 95% confidence interval is 0.0139. There are 3 homozygotes in GnomAd4. There are 255 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 3 AD,AR,SD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130837.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OPA1	NM_130837.3	MANE Select	c.43C>A	p.Gln15Lys	missense	Exon 2 of 31	NP_570850.2	O60313-10
OPA1	NM_130836.3		c.43C>A	p.Gln15Lys	missense	Exon 2 of 30	NP_570849.2	O60313-2
OPA1	NM_130835.3		c.43C>A	p.Gln15Lys	missense	Exon 2 of 30	NP_570848.1	E5KLJ9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OPA1	ENST00000361510.8	TSL:5 MANE Select	c.43C>A	p.Gln15Lys	missense	Exon 2 of 31	ENSP00000355324.2	O60313-10
OPA1	ENST00000361908.8	TSL:1	c.43C>A	p.Gln15Lys	missense	Exon 2 of 30	ENSP00000354681.3	O60313-2
OPA1	ENST00000968586.1		c.43C>A	p.Gln15Lys	missense	Exon 2 of 32	ENSP00000638645.1

Frequencies

GnomAD3 genomes

AF:

0.00308

AC:

469

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00282

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.0162

Gnomad SAS

AF:

0.0170

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00254

Gnomad OTH

AF:

0.00716

GnomAD2 exomes

AF:

0.00645

AC:

1605

AN:

248890

AF XY:

0.00783

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.00231

Gnomad ASJ exome

AF:

0.00586

Gnomad EAS exome

AF:

0.0176

Gnomad FIN exome

AF:

0.00134

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00540

GnomAD4 exome

AF:

0.00426

AC:

6215

AN:

1460454

Hom.:

Cov.:

AF XY:

0.00506

AC XY:

3680

AN XY:

726652

show subpopulations

African (AFR)

AF:

0.000807

AC:

AN:

33448

American (AMR)

AF:

0.00226

AC:

101

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00670

AC:

175

AN:

26132

East Asian (EAS)

AF:

0.0236

AC:

937

AN:

39682

South Asian (SAS)

AF:

0.0238

AC:

2053

AN:

86214

European-Finnish (FIN)

AF:

0.00168

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.0186

AC:

107

AN:

5766

European-Non Finnish (NFE)

AF:

0.00218

AC:

2424

AN:

1110724

Other (OTH)

AF:

0.00499

AC:

301

AN:

60344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.447

Heterozygous variant carriers

336

672

1009

1345

1681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

106

212

318

424

530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00307

AC:

467

AN:

152260

Hom.:

Cov.:

AF XY:

0.00343

AC XY:

255

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.000626

AC:

AN:

41560

American (AMR)

AF:

0.00281

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00749

AC:

AN:

3470

East Asian (EAS)

AF:

0.0162

AC:

AN:

5180

South Asian (SAS)

AF:

0.0168

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00151

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00254

AC:

173

AN:

68016

Other (OTH)

AF:

0.00662

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

100

125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00385

Hom.:

Bravo

AF:

0.00320

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00407

AC:

ExAC

AF:

0.00675

AC:

819

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.00463

EpiControl

AF:

0.00492

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Autosomal dominant optic atrophy classic form (2)

not specified (2)

Abortive cerebellar ataxia (1)

Mitochondrial DNA depletion syndrome 14 (cardioencephalomyopathic type) (1)

Optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.18

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.0065

Eigen

Benign

-0.050

Eigen_PC

Benign

0.17

FATHMM_MKL

Uncertain

0.85

LIST_S2

Uncertain

0.91

MetaRNN

Benign

0.0065

MetaSVM

Benign

-0.68

MutationAssessor

Benign

0.69

PhyloP100

3.4

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-0.17

REVEL

Benign

0.22

Sift

Benign

0.30

Sift4G

Benign

0.35

Polyphen

0.0

Vest4

0.49

MVP

0.74

MPC

0.12

ClinPred

0.0053

GERP RS

5.1

Varity_R

0.34

gMVP

0.40

Mutation Taster

=98/2

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over