Variant chr10-13108909-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001008212.2(OPTN):c.-11-203T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 592,040 control chromosomes in the GnomAD database, including 38,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 9589 hom., cov: 30)

Exomes 𝑓: 0.36 ( 28940 hom. )

Consequence

OPTN
NM_001008212.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.00

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:

OPTN (HGNC:):

OPTN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-13108909-T-C is Benign according to our data. Variant chr10-13108909-T-C is described in ClinVar as [Benign]. Clinvar id is 1295362.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
OPTN	NM_001008212.2 linkuse as main transcript	c.-11-203T>C	intron_variant	ENST00000378747.8	NP_001008213.1	Q96CV9-1
OPTN	NM_001008211.1 linkuse as main transcript	c.-80-53T>C	intron_variant		NP_001008212.1	Q96CV9-1
OPTN	NM_001008213.1 linkuse as main transcript	c.-65-53T>C	intron_variant		NP_001008214.1	Q96CV9-1
OPTN	NM_021980.4 linkuse as main transcript	c.-11-203T>C	intron_variant		NP_068815.2	Q96CV9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPTN	ENST00000378747.8 linkuse as main transcript	c.-11-203T>C		intron_variant		1	NM_001008212.2	ENSP00000368021.3		Q96CV9-1

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

53946

AN:

151286

Hom.:

9581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.392

GnomAD4 exome

AF:

0.361

AC:

158923

AN:

440640

Hom.:

28940

AF XY:

0.361

AC XY:

85095

AN XY:

235396

show subpopulations

Gnomad4 AFR exome

AF:

0.336

Gnomad4 AMR exome

AF:

0.389

Gnomad4 ASJ exome

AF:

0.428

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.254

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.367

GnomAD4 genome

AF:

0.356

AC:

53969

AN:

151400

Hom.:

9589

Cov.:

AF XY:

0.356

AC XY:

26303

AN XY:

73980

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.391

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.497

Gnomad4 SAS

AF:

0.397

Gnomad4 FIN

AF:

0.251

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.396

Alfa

AF:

0.352

Hom.:

1154

Bravo

AF:

0.368

Asia WGS

AF:

0.490

AC:

1703

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 18, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.4

DANN

Benign

0.10

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.97

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