Variant X-154187964-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_000513.2(OPN1MW):c.307A>G(p.Thr103Ala) 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 (★).

Frequency

Genomes: 𝑓 0.0066 ( 2 hom., 3 hem., cov: 3)

Exomes 𝑓: 0.0054 ( 73 hom. 148 hem. )

Failed GnomAD Quality Control

Consequence

OPN1MW
NM_000513.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.83

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:

OPN1MW (HGNC:):

OPN1MW links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038114786).

BP6

Variant X-154187964-A-G is Benign according to our data. Variant chrX-154187964-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2661789.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-154187964-A-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OPN1MW	NM_000513.2 linkuse as main transcript	c.307A>G	p.Thr103Ala	missense_variant	2/6	ENST00000595290.6	NP_000504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OPN1MW	ENST00000595290.6 linkuse as main transcript	c.307A>G	p.Thr103Ala	missense_variant	2/6	1	NM_000513.2	ENSP00000472316.1		P04001
OPN1MW	ENST00000595330.1 linkuse as main transcript	n.317A>G		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

206

AN:

31066

Hom.:

Cov.:

AF XY:

0.000679

AC XY:

AN XY:

4416

FAILED QC

Gnomad AFR

AF:

0.00181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.00126

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00727

Gnomad OTH

AF:

0.00641

GnomAD3 exomes

AF:

0.00558

AC:

330

AN:

59187

Hom.:

AF XY:

0.000747

AC XY:

AN XY:

13385

show subpopulations

Gnomad AFR exome

AF:

0.00326

Gnomad AMR exome

AF:

0.00608

Gnomad ASJ exome

AF:

0.0177

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00316

Gnomad NFE exome

AF:

0.00679

Gnomad OTH exome

AF:

0.00506

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00542

AC:

3690

AN:

680657

Hom.:

Cov.:

AF XY:

0.000829

AC XY:

148

AN XY:

178503

show subpopulations

Gnomad4 AFR exome

AF:

0.00185

Gnomad4 AMR exome

AF:

0.00370

Gnomad4 ASJ exome

AF:

0.0157

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000175

Gnomad4 FIN exome

AF:

0.00169

Gnomad4 NFE exome

AF:

0.00587

Gnomad4 OTH exome

AF:

0.00656

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00663

AC:

206

AN:

31053

Hom.:

Cov.:

AF XY:

0.000680

AC XY:

AN XY:

4415

show subpopulations

Gnomad4 AFR

AF:

0.00181

Gnomad4 AMR

AF:

0.0107

Gnomad4 ASJ

AF:

0.0193

Gnomad4 EAS

AF:

0.00127

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00188

Gnomad4 NFE

AF:

0.00728

Gnomad4 OTH

AF:

0.00639

Alfa

AF:

0.00449

Hom.:

ExAC

AF:

0.00404

AC:

297

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

Feb 01, 2024

OPN1MW: PP2, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.055

FATHMM_MKL

Uncertain

0.83

MetaRNN

Benign

0.0038

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.60

Sift4G

Benign

0.36

Polyphen

0.17

Vest4

0.097

MVP

0.95

ClinPred

0.0099

GERP RS

2.9

Varity_R

0.26

gMVP

0.71

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