Variant 1-203496268-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+32T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,504,090 control chromosomes in the GnomAD database, including 122,013 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 10930 hom., cov: 32)

Exomes 𝑓: 0.40 ( 111083 hom. )

Consequence

OPTC
NM_014359.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.111

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=-0.86).

BP6

Variant 1-203496268-T-C is Benign according to our data. Variant chr1-203496268-T-C is described in ClinVar as [Benign]. Clinvar id is 1230152.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPTC	NM_014359.4 link	c.231+32T>C		intron_variant		ENST00000367222.7	NP_055174.1	Q9UBM4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPTC	ENST00000367222.7 link	c.231+32T>C		intron_variant		1	NM_014359.4	ENSP00000356191.2		Q9UBM4
OPTC	ENST00000448911.1 link	c.231+32T>C		intron_variant		2		ENSP00000399491.2		Q5T2G3

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57069

AN:

151934

Hom.:

10931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.550

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.352

GnomAD3 exomes

AF:

0.397

AC:

97169

AN:

244740

Hom.:

19641

AF XY:

0.399

AC XY:

52890

AN XY:

132472

show subpopulations

Gnomad AFR exome

AF:

0.310

Gnomad AMR exome

AF:

0.329

Gnomad ASJ exome

AF:

0.399

Gnomad EAS exome

AF:

0.478

Gnomad SAS exome

AF:

0.395

Gnomad FIN exome

AF:

0.483

Gnomad NFE exome

AF:

0.402

Gnomad OTH exome

AF:

0.382

GnomAD4 exome

AF:

0.404

AC:

545937

AN:

1352038

Hom.:

111083

Cov.:

AF XY:

0.403

AC XY:

273537

AN XY:

678362

show subpopulations

Gnomad4 AFR exome

AF:

0.308

Gnomad4 AMR exome

AF:

0.331

Gnomad4 ASJ exome

AF:

0.400

Gnomad4 EAS exome

AF:

0.512

Gnomad4 SAS exome

AF:

0.395

Gnomad4 FIN exome

AF:

0.478

Gnomad4 NFE exome

AF:

0.404

Gnomad4 OTH exome

AF:

0.394

GnomAD4 genome

AF:

0.376

AC:

57121

AN:

152052

Hom.:

10930

Cov.:

AF XY:

0.379

AC XY:

28191

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.310

Gnomad4 AMR

AF:

0.326

Gnomad4 ASJ

AF:

0.383

Gnomad4 EAS

AF:

0.476

Gnomad4 SAS

AF:

0.402

Gnomad4 FIN

AF:

0.483

Gnomad4 NFE

AF:

0.399

Gnomad4 OTH

AF:

0.351

Alfa

AF:

0.312

Hom.:

1314

Bravo

AF:

0.360

Asia WGS

AF:

0.459

AC:

1599

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	clinical testing	GeneDx	Jun 26, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.2

DANN

Benign

0.65

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