Variant chr1-203496342-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_014359.4(OPTC):c.231+106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 773,624 control chromosomes in the GnomAD database, including 945 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 156 hom., cov: 32)

Exomes 𝑓: 0.044 ( 789 hom. )

Consequence

OPTC
NM_014359.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0800

Variant links:

Genes affected

OPTC (HGNC:8158): (opticin) Opticin belongs to class III of the small leucine-rich repeat protein (SLRP) family. Members of this family are typically associated with the extracellular matrix. Opticin is present in significant quantities in the vitreous of the eye and also localizes to the cornea, iris, ciliary body, optic nerve, choroid, retina, and fetal liver. Opticin may noncovalently bind collagen fibrils and regulate fibril morphology, spacing, and organization. The opticin gene is mapped to a region of chromosome 1 that is associated with the inherited eye diseases age-related macular degeneration (AMD) and posterior column ataxia with retinosa pigmentosa (AXPC1). [provided by RefSeq, Jul 2008]

OPTC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-203496342-T-C is Benign according to our data. Variant chr1-203496342-T-C is described in ClinVar as [Benign]. Clinvar id is 1291763.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPTC	NM_014359.4 linkuse as main transcript	c.231+106T>C		intron_variant		ENST00000367222.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPTC	ENST00000367222.7 linkuse as main transcript	c.231+106T>C		intron_variant		1	NM_014359.4	P1
OPTC	ENST00000448911.1 linkuse as main transcript	c.231+106T>C		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0377

AC:

5729

AN:

152152

Hom.:

156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0109

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.0380

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.0234

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0583

Gnomad OTH

AF:

0.0407

GnomAD4 exome

AF:

0.0442

AC:

27479

AN:

621354

Hom.:

789

AF XY:

0.0442

AC XY:

14703

AN XY:

332962

show subpopulations

Gnomad4 AFR exome

AF:

0.00979

Gnomad4 AMR exome

AF:

0.0270

Gnomad4 ASJ exome

AF:

0.0572

Gnomad4 EAS exome

AF:

0.0000600

Gnomad4 SAS exome

AF:

0.0282

Gnomad4 FIN exome

AF:

0.0261

Gnomad4 NFE exome

AF:

0.0554

Gnomad4 OTH exome

AF:

0.0456

GnomAD4 genome

AF:

0.0376

AC:

5732

AN:

152270

Hom.:

156

Cov.:

AF XY:

0.0362

AC XY:

2699

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0109

Gnomad4 AMR

AF:

0.0380

Gnomad4 ASJ

AF:

0.0542

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0199

Gnomad4 FIN

AF:

0.0234

Gnomad4 NFE

AF:

0.0583

Gnomad4 OTH

AF:

0.0403

Alfa

AF:

0.0462

Hom.:

Bravo

AF:

0.0372

Asia WGS

AF:

0.00808

AC:

AN:

3478

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	Jun 26, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.1

DANN

Benign

0.63

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