Variant 1-203496264-T-G 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+28T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 1,542,504 control chromosomes in the GnomAD database, including 3,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.093 ( 964 hom., cov: 32)

Exomes 𝑓: 0.052 ( 2544 hom. )

Consequence

OPTC
NM_014359.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.285

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 1-203496264-T-G is Benign according to our data. Variant chr1-203496264-T-G is described in ClinVar as [Benign]. Clinvar id is 1269950.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 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+28T>G		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+28T>G		intron_variant		1	NM_014359.4	P1
OPTC	ENST00000448911.1 linkuse as main transcript	c.231+28T>G		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0932

AC:

14171

AN:

152050

Hom.:

965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0804

Gnomad ASJ

AF:

0.0599

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.0587

Gnomad FIN

AF:

0.0437

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0451

Gnomad OTH

AF:

0.0923

GnomAD3 exomes

AF:

0.0708

AC:

17491

AN:

246960

Hom.:

918

AF XY:

0.0671

AC XY:

8975

AN XY:

133704

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.0760

Gnomad ASJ exome

AF:

0.0596

Gnomad EAS exome

AF:

0.184

Gnomad SAS exome

AF:

0.0534

Gnomad FIN exome

AF:

0.0403

Gnomad NFE exome

AF:

0.0453

Gnomad OTH exome

AF:

0.0629

GnomAD4 exome

AF:

0.0515

AC:

71642

AN:

1390336

Hom.:

2544

Cov.:

AF XY:

0.0508

AC XY:

35377

AN XY:

695926

show subpopulations

Gnomad4 AFR exome

AF:

0.195

Gnomad4 AMR exome

AF:

0.0738

Gnomad4 ASJ exome

AF:

0.0601

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.0516

Gnomad4 FIN exome

AF:

0.0412

Gnomad4 NFE exome

AF:

0.0424

Gnomad4 OTH exome

AF:

0.0613

GnomAD4 genome

AF:

0.0931

AC:

14172

AN:

152168

Hom.:

964

Cov.:

AF XY:

0.0924

AC XY:

6872

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.189

Gnomad4 AMR

AF:

0.0802

Gnomad4 ASJ

AF:

0.0599

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.0585

Gnomad4 FIN

AF:

0.0437

Gnomad4 NFE

AF:

0.0452

Gnomad4 OTH

AF:

0.0899

Alfa

AF:

0.0685

Hom.:

Bravo

AF:

0.101

Asia WGS

AF:

0.0900

AC:

314

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

-0.86

CADD

Benign

2.6

DANN

Benign

0.26

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