Variant rs11202106 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_033282.4(OPN4):c.30G>A(p.Pro10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,352,062 control chromosomes in the GnomAD database, including 62,460 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P10P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.25 ( 5415 hom., cov: 32)

Exomes 𝑓: 0.36 ( 57045 hom. )

Consequence

OPN4
NM_033282.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.12

Variant links:

Genes affected

OPN4 (HGNC:14449): (opsin 4) Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. This gene encodes a photoreceptive opsin protein that is expressed within the ganglion and amacrine cell layers of the retina. In mouse, retinal ganglion cell axons expressing this gene projected to the suprachiasmatic nucleus and other brain nuclei involved in circadian photoentrainment. In mouse, this protein is coupled to a transient receptor potential (TRP) ion channel through a G protein signaling pathway and produces a physiologic light response via membrane depolarization and increased intracellular calcium. The protein functions as a sensory photopigment and may also have photoisomerase activity. Experiments with knockout mice indicate that this gene attenuates, but does not abolish, photoentrainment. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

OPN4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP7

Synonymous conserved (PhyloP=-6.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
OPN4	NM_033282.4 linkuse as main transcript	c.30G>A	p.Pro10=	synonymous_variant	1/10	ENST00000241891.10	NP_150598.1
OPN4	NM_001030015.3 linkuse as main transcript	c.30G>A	p.Pro10=	synonymous_variant	1/11		NP_001025186.1
OPN4	XM_017016955.2 linkuse as main transcript	c.30G>A	p.Pro10=	synonymous_variant	1/10		XP_016872444.1
OPN4	XM_017016956.2 linkuse as main transcript	c.30G>A	p.Pro10=	synonymous_variant	1/9		XP_016872445.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPN4	ENST00000241891.10 linkuse as main transcript	c.30G>A	p.Pro10=	synonymous_variant	1/10	1	NM_033282.4	ENSP00000241891	P1	Q9UHM6-1
OPN4	ENST00000372071.7 linkuse as main transcript	c.30G>A	p.Pro10=	synonymous_variant	1/11	1		ENSP00000361141		Q9UHM6-2
OPN4	ENST00000690949.1 linkuse as main transcript	n.145+151G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

37538

AN:

147736

Hom.:

5408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.351

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.215

GnomAD3 exomes

AF:

0.288

AC:

72297

AN:

250662

Hom.:

11489

AF XY:

0.301

AC XY:

40844

AN XY:

135588

show subpopulations

Gnomad AFR exome

AF:

0.0943

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.344

Gnomad EAS exome

AF:

0.256

Gnomad SAS exome

AF:

0.408

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.318

Gnomad OTH exome

AF:

0.278

GnomAD4 exome

AF:

0.359

AC:

431962

AN:

1204204

Hom.:

57045

Cov.:

AF XY:

0.361

AC XY:

218496

AN XY:

604612

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.168

Gnomad4 ASJ exome

AF:

0.380

Gnomad4 EAS exome

AF:

0.343

Gnomad4 SAS exome

AF:

0.415

Gnomad4 FIN exome

AF:

0.366

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.254

AC:

37558

AN:

147858

Hom.:

5415

Cov.:

AF XY:

0.256

AC XY:

18454

AN XY:

72096

show subpopulations

Gnomad4 AFR

AF:

0.100

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.295

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.351

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.292

Hom.:

2927

Bravo

AF:

0.223

Asia WGS

AF:

0.328

AC:

1140

AN:

3478

EpiCase

AF:

0.304

EpiControl

AF:

0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.61

DANN

Benign

0.36

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over