Variant X-154154684-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_020061.6(OPN1LW):c.689T>C(p.Ile230Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00296 in 1,188,737 control chromosomes in the GnomAD database, including 10 homozygotes. There are 191 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., 9 hem., cov: 17)

Exomes 𝑓: 0.0030 ( 10 hom. 182 hem. )

Consequence

OPN1LW
NM_020061.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.06

Variant links:

Genes affected

OPN1LW (HGNC:9936): (opsin 1, long wave sensitive) This gene encodes for a light absorbing visual pigment of the opsin gene family. The encoded protein is called red cone photopigment or long-wavelength sensitive opsin. Opsins are G-protein coupled receptors with seven transmembrane domains, an N-terminal extracellular domain, and a C-terminal cytoplasmic domain. This gene and the medium-wavelength opsin gene are tandemly arrayed on the X chromosome and frequent unequal recombination and gene conversion may occur between these sequences. X chromosomes may have fusions of the medium- and long-wavelength opsin genes or may have more than one copy of these genes. Defects in this gene are the cause of partial, protanopic colorblindness. [provided by RefSeq, Jul 2008]

OPN1LW links:

OPN1LW (HGNC:):

OPN1LW links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.016978055).

BP6

Variant X-154154684-T-C is Benign according to our data. Variant chrX-154154684-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2661787.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-154154684-T-C is described in Lovd as [Benign].

BS2

High Hemizygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPN1LW	NM_020061.6 linkuse as main transcript	c.689T>C	p.Ile230Thr	missense_variant	4/6	ENST00000369951.9	NP_064445.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
OPN1LW	ENST00000369951.9 linkuse as main transcript	c.689T>C	p.Ile230Thr	missense_variant	4/6	1	NM_020061.6	ENSP00000358967.4	P04000
OPN1LW	ENST00000442922.1 linkuse as main transcript	c.278T>C	p.Ile93Thr	missense_variant	2/4	5		ENSP00000402493.1	H0Y622
OPN1LW	ENST00000463296.1 linkuse as main transcript	n.588+1576T>C		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00244

AC:

260

AN:

106704

Hom.:

Cov.:

AF XY:

0.000303

AC XY:

AN XY:

29692

show subpopulations

Gnomad AFR

AF:

0.00105

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00104

Gnomad ASJ

AF:

0.00396

Gnomad EAS

AF:

0.000589

Gnomad SAS

AF:

0.000830

Gnomad FIN

AF:

0.000728

Gnomad MID

AF:

0.00429

Gnomad NFE

AF:

0.00388

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00232

AC:

418

AN:

180224

Hom.:

AF XY:

0.000461

AC XY:

AN XY:

65072

show subpopulations

Gnomad AFR exome

AF:

0.00107

Gnomad AMR exome

AF:

0.00146

Gnomad ASJ exome

AF:

0.00234

Gnomad EAS exome

AF:

0.000946

Gnomad SAS exome

AF:

0.000907

Gnomad FIN exome

AF:

0.000954

Gnomad NFE exome

AF:

0.00362

Gnomad OTH exome

AF:

0.00269

GnomAD4 exome

AF:

0.00301

AC:

3253

AN:

1081981

Hom.:

Cov.:

AF XY:

0.000522

AC XY:

182

AN XY:

348799

show subpopulations

Gnomad4 AFR exome

AF:

0.000914

Gnomad4 AMR exome

AF:

0.00160

Gnomad4 ASJ exome

AF:

0.00281

Gnomad4 EAS exome

AF:

0.00174

Gnomad4 SAS exome

AF:

0.00126

Gnomad4 FIN exome

AF:

0.00156

Gnomad4 NFE exome

AF:

0.00336

Gnomad4 OTH exome

AF:

0.00295

GnomAD4 genome

AF:

0.00244

AC:

260

AN:

106756

Hom.:

Cov.:

AF XY:

0.000302

AC XY:

AN XY:

29754

show subpopulations

Gnomad4 AFR

AF:

0.00105

Gnomad4 AMR

AF:

0.00104

Gnomad4 ASJ

AF:

0.00396

Gnomad4 EAS

AF:

0.000591

Gnomad4 SAS

AF:

0.000832

Gnomad4 FIN

AF:

0.000728

Gnomad4 NFE

AF:

0.00388

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00292

Hom.:

ESP6500AA

AF:

0.000786

AC:

ESP6500EA

AF:

0.00285

AC:

ExAC

AF:

0.00291

AC:

350

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2023

OPN1LW: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.63

CADD

Benign

4.3

DANN

Benign

0.70

FATHMM_MKL

Uncertain

0.93

LIST_S2

Benign

0.67

.;T

M_CAP

Benign

0.055

MetaRNN

Benign

0.017

T;T

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.58

PROVEAN

Uncertain

-2.5

D;D

REVEL

Benign

0.13

Sift

Benign

0.094

T;D

Sift4G

Benign

0.12

T;T

Vest4

0.12

MVP

0.47

MPC

0.90

ClinPred

0.016

GERP RS

1.8

gMVP

0.73

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