Genetic Variant OPN1SW:p.Gly119Gly (chr7-128775141-T-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001385125.1(OPN1SW):c.357A>C(p.Gly119Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,613,548 control chromosomes in the GnomAD database, including 114,691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7853 hom., cov: 32)

Exomes 𝑓: 0.37 ( 106838 hom. )

Consequence

OPN1SW
NM_001385125.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.513

Variant links:

Genes affected

OPN1SW (HGNC:1012): (opsin 1, short wave sensitive) This gene belongs to the G-protein coupled receptor 1 family, opsin subfamily. It encodes the blue cone pigment gene which is one of three types of cone photoreceptors responsible for normal color vision. Defects in this gene are the cause of tritan color blindness (tritanopia). Affected individuals lack blue and yellow sensory mechanisms while retaining those for red and green. Defective blue vision is characteristic. [provided by RefSeq, Jul 2008]

OPN1SW links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 7-128775141-T-G is Benign according to our data. Variant chr7-128775141-T-G is described in ClinVar as [Benign]. Clinvar id is 1169097.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-128775141-T-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.513 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPN1SW	NM_001385125.1 link	c.357A>C	p.Gly119Gly	synonymous_variant	Exon 2 of 5	ENST00000249389.3	NP_001372054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPN1SW	ENST00000249389.3 link	c.357A>C	p.Gly119Gly	synonymous_variant	Exon 2 of 5	1	NM_001385125.1	ENSP00000249389.3		P03999

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

45006

AN:

152004

Hom.:

7849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.0680

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.321

GnomAD3 exomes

AF:

0.301

AC:

75425

AN:

250374

Hom.:

13024

AF XY:

0.309

AC XY:

41810

AN XY:

135328

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.225

Gnomad ASJ exome

AF:

0.372

Gnomad EAS exome

AF:

0.0572

Gnomad SAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.323

Gnomad NFE exome

AF:

0.401

Gnomad OTH exome

AF:

0.341

GnomAD4 exome

AF:

0.371

AC:

542730

AN:

1461426

Hom.:

106838

Cov.:

AF XY:

0.368

AC XY:

267793

AN XY:

726972

show subpopulations

Gnomad4 AFR exome

AF:

0.141

Gnomad4 AMR exome

AF:

0.229

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.0612

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.328

Gnomad4 NFE exome

AF:

0.411

Gnomad4 OTH exome

AF:

0.343

GnomAD4 genome

AF:

0.296

AC:

45008

AN:

152122

Hom.:

7853

Cov.:

AF XY:

0.290

AC XY:

21595

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.147

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.376

Gnomad4 EAS

AF:

0.0687

Gnomad4 SAS

AF:

0.197

Gnomad4 FIN

AF:

0.335

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.317

Alfa

AF:

0.372

Hom.:

6460

Bravo

AF:

0.288

Asia WGS

AF:

0.127

AC:

443

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Blue color blindness

Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

OPN1SW-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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