10-13109245-G-A

Position:

chr10-13109245-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The ENST00000378747.8(OPTN):c.123G>A(p.Leu41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.01 in 1,613,908 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0071 ( 6 hom., cov: 30)

Exomes 𝑓: 0.010 ( 85 hom. )

Consequence

OPTN
ENST00000378747.8 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 1.03

Variant links:

Genes affected

OPTN (HGNC:17142): (optineurin) This gene encodes the coiled-coil containing protein optineurin. Optineurin may play a role in normal-tension glaucoma and adult-onset primary open angle glaucoma. Optineurin interacts with adenovirus E3-14.7K protein and may utilize tumor necrosis factor-alpha or Fas-ligand pathways to mediate apoptosis, inflammation or vasoconstriction. Optineurin may also function in cellular morphogenesis and membrane trafficking, vesicle trafficking, and transcription activation through its interactions with the RAB8, huntingtin, and transcription factor IIIA proteins. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

OPTN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 10-13109245-G-A is Benign according to our data. Variant chr10-13109245-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 96023.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-13109245-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.03 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00709 (1079/152216) while in subpopulation NFE AF= 0.0118 (804/68004). AF 95% confidence interval is 0.0111. There are 6 homozygotes in gnomad4. There are 518 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
OPTN	NM_001008212.2 linkuse as main transcript	c.123G>A	p.Leu41=	synonymous_variant	3/15	ENST00000378747.8	NP_001008213.1
OPTN	NM_001008211.1 linkuse as main transcript	c.123G>A	p.Leu41=	synonymous_variant	4/16		NP_001008212.1
OPTN	NM_001008213.1 linkuse as main transcript	c.123G>A	p.Leu41=	synonymous_variant	4/16		NP_001008214.1
OPTN	NM_021980.4 linkuse as main transcript	c.123G>A	p.Leu41=	synonymous_variant	2/14		NP_068815.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPTN	ENST00000378747.8 linkuse as main transcript	c.123G>A	p.Leu41=	synonymous_variant	3/15	1	NM_001008212.2	ENSP00000368021	P3	Q96CV9-1

Frequencies

GnomAD3 genomes

AF:

0.00709

AC:

1079

AN:

152098

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00188

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00183

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00208

Gnomad FIN

AF:

0.0130

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.00623

GnomAD3 exomes

AF:

0.00719

AC:

1807

AN:

251220

Hom.:

AF XY:

0.00702

AC XY:

953

AN XY:

135792

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00318

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.00140

Gnomad FIN exome

AF:

0.0132

Gnomad NFE exome

AF:

0.0113

Gnomad OTH exome

AF:

0.00620

GnomAD4 exome

AF:

0.0103

AC:

15064

AN:

1461692

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

7287

AN XY:

727136

show subpopulations

Gnomad4 AFR exome

AF:

0.00155

Gnomad4 AMR exome

AF:

0.00277

Gnomad4 ASJ exome

AF:

0.00149

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.00165

Gnomad4 FIN exome

AF:

0.0126

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.00926

GnomAD4 genome

AF:

0.00709

AC:

1079

AN:

152216

Hom.:

Cov.:

AF XY:

0.00696

AC XY:

518

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.00188

Gnomad4 AMR

AF:

0.00183

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00229

Gnomad4 FIN

AF:

0.0130

Gnomad4 NFE

AF:

0.0118

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00944

Hom.:

Bravo

AF:

0.00652

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0103

EpiControl

AF:

0.00836

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 13, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 28, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2024	OPTN: BP4, BP7, BS1, BS2 -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Sep 10, 2013

- -

Amyotrophic lateral sclerosis type 12

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Inborn genetic diseases

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 11, 2019

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Primary open angle glaucoma;C1842026:Glaucoma 1, open angle, E;C3150692:Amyotrophic lateral sclerosis type 12

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Primary open angle glaucoma

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

6.4

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over