Variant X-154187851-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

The NM_000513.2(OPN1MW):c.194T>C(p.Ile65Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0079 ( 1 hom., 1 hem., cov: 1)

Exomes 𝑓: 0.0079 ( 208 hom. 364 hem. )

Failed GnomAD Quality Control

Consequence

OPN1MW
NM_000513.2 missense

Scores

Clinical Significance

Benign/Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 0.451

Variant links:

Genes affected

OPN1MW (HGNC:4206): (opsin 1, medium wave sensitive) This gene encodes for a light absorbing visual pigment of the opsin gene family. The encoded protein is called green cone photopigment or medium-wavelength sensitive opsin. Opsins are G-protein coupled receptors with seven transmembrane domains, an N-terminal extracellular domain, and a C-terminal cytoplasmic domain. The long-wavelength opsin gene and multiple copies of 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 deutanopic colorblindness. [provided by RefSeq, Mar 2009]

OPN1MW links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013074905).

BP6

Variant X-154187851-T-C is Benign according to our data. Variant chrX-154187851-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1284388.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-154187851-T-C is described in Lovd as [Benign]. Variant chrX-154187851-T-C is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPN1MW	NM_000513.2 linkuse as main transcript	c.194T>C	p.Ile65Thr	missense_variant	2/6	ENST00000595290.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPN1MW	ENST00000595290.6 linkuse as main transcript	c.194T>C	p.Ile65Thr	missense_variant	2/6	1	NM_000513.2	P1
OPN1MW	ENST00000595330.1 linkuse as main transcript	n.204T>C		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

122

AN:

15426

Hom.:

Cov.:

AF XY:

0.000639

AC XY:

AN XY:

1564

FAILED QC

Gnomad AFR

AF:

0.00766

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0126

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00543

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00884

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00794

AC:

2573

AN:

324178

Hom.:

208

Cov.:

AF XY:

0.00417

AC XY:

364

AN XY:

87388

show subpopulations

Gnomad4 AFR exome

AF:

0.0224

Gnomad4 AMR exome

AF:

0.00700

Gnomad4 ASJ exome

AF:

0.00147

Gnomad4 EAS exome

AF:

0.00245

Gnomad4 SAS exome

AF:

0.00456

Gnomad4 FIN exome

AF:

0.0103

Gnomad4 NFE exome

AF:

0.00850

Gnomad4 OTH exome

AF:

0.00764

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00791

AC:

122

AN:

15426

Hom.:

Cov.:

AF XY:

0.000639

AC XY:

AN XY:

1564

show subpopulations

Gnomad4 AFR

AF:

0.00766

Gnomad4 AMR

AF:

0.0125

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00543

Gnomad4 NFE

AF:

0.00884

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00309

Hom.:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Clinical Genetics, Academic Medical Center

- -

not provided

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.3

DANN

Benign

0.63

DEOGEN2

Benign

0.093

FATHMM_MKL

Benign

0.13

M_CAP

Benign

0.0045

MetaRNN

Benign

0.013

MetaSVM

Benign

-0.95

MutationTaster

Benign

0.99

PrimateAI

Uncertain

0.75

Sift4G

Benign

0.13

Polyphen

0.0

Vest4

0.17

MVP

0.27

ClinPred

0.0061

GERP RS

2.9

Varity_R

0.024

gMVP

0.54

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