Variant X-154150890-C-A 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.347C>A(p.Ser116Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000462 in 1,192,456 control chromosomes in the GnomAD database, including 16 homozygotes. There are 242 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict 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 0.00032 ( 1 hom., 5 hem., cov: 18)

Exomes 𝑓: 0.00048 ( 15 hom. 237 hem. )

Consequence

OPN1LW
NM_020061.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.424

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=0.022827089).

BP6

Variant X-154150890-C-A is Benign according to our data. Variant chrX-154150890-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661786.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-154150890-C-A is described in Lovd as [Benign]. Variant chrX-154150890-C-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPN1LW	NM_020061.6 linkuse as main transcript	c.347C>A	p.Ser116Tyr	missense_variant	2/6	ENST00000369951.9	NP_064445.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPN1LW	ENST00000369951.9 linkuse as main transcript	c.347C>A	p.Ser116Tyr	missense_variant	2/6	1	NM_020061.6	ENSP00000358967.4		P04000
OPN1LW	ENST00000463296.1 linkuse as main transcript	n.357C>A		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes

AF:

0.000320

AC:

AN:

106090

Hom.:

Cov.:

AF XY:

0.000166

AC XY:

AN XY:

30046

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000988

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000519

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000344

Gnomad OTH

AF:

0.00208

GnomAD3 exomes

AF:

0.000505

AC:

AN:

180327

Hom.:

AF XY:

0.000611

AC XY:

AN XY:

65477

show subpopulations

Gnomad AFR exome

AF:

0.0000772

Gnomad AMR exome

AF:

0.00114

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000363

Gnomad SAS exome

AF:

0.000317

Gnomad FIN exome

AF:

0.000766

Gnomad NFE exome

AF:

0.000400

Gnomad OTH exome

AF:

0.000895

GnomAD4 exome

AF:

0.000476

AC:

517

AN:

1086335

Hom.:

Cov.:

AF XY:

0.000671

AC XY:

237

AN XY:

352999

show subpopulations

Gnomad4 AFR exome

AF:

0.0000384

Gnomad4 AMR exome

AF:

0.00111

Gnomad4 ASJ exome

AF:

0.0000527

Gnomad4 EAS exome

AF:

0.000999

Gnomad4 SAS exome

AF:

0.000485

Gnomad4 FIN exome

AF:

0.00227

Gnomad4 NFE exome

AF:

0.000367

Gnomad4 OTH exome

AF:

0.000461

GnomAD4 genome

AF:

0.000320

AC:

AN:

106121

Hom.:

Cov.:

AF XY:

0.000166

AC XY:

AN XY:

30089

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000987

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000519

Gnomad4 NFE

AF:

0.000344

Gnomad4 OTH

AF:

0.00206

Alfa

AF:

0.00123

Hom.:

ExAC

AF:

0.000773

AC:

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

Apr 01, 2023

OPN1LW: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.0010

DANN

Benign

0.33

FATHMM_MKL

Benign

0.0047

M_CAP

Benign

0.0043

MetaRNN

Benign

0.023

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.39

PROVEAN

Benign

0.24

REVEL

Benign

0.053

Sift

Benign

0.38

Sift4G

Benign

1.0

Vest4

0.044

MVP

0.043

MPC

0.88

ClinPred

0.0017

GERP RS

-0.091

gMVP

0.66

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