X-154190109-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6 BP7 BS2

The NM_000513.2(OPN1MW):c.465C>G(p.Val155=) variant causes a synonymous 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: not found (cov: 0)
  • Failed GnomAD Quality Control
• Consequence: OPN1MW NM_000513.2 synonymous
• Clinical Significance: Likely benign no assertion criteria provided B:2
• Conservation: PhyloP100: -0.291

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP6: Variant X-154190109-C-G is Benign according to our data. Variant chrX-154190109-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1284421.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-154190109-C-G is described in Lovd as [Likely_benign].
• BP7: Synonymous conserved (PhyloP=-0.291 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome at 102 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPN1MW	NM_000513.2	c.465C>G	p.Val155=	synonymous_variant	3/6	ENST00000595290.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPN1MW	ENST00000595290.6	c.465C>G	p.Val155=	synonymous_variant	3/6	1	NM_000513.2	P1
OPN1MW	ENST00000596998.2	c.54C>G	p.Val18=	synonymous_variant	1/4	5
OPN1MW	ENST00000595330.1	n.475C>G		non_coding_transcript_exon_variant	3/4	5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0372 AC: 516 AN: 13880 Hom.: 102 AF XY: 0.0245 AC XY: 69 AN XY: 2820

Gnomad AFR exome AF: 0.0409

Gnomad AMR exome AF: 0.0985

Gnomad ASJ exome AF: 0.0176

Gnomad EAS exome AF: 0.0307

Gnomad SAS exome AF: 0.0322

Gnomad FIN exome AF: 0.0121

Gnomad NFE exome AF: 0.0264

Gnomad OTH exome AF: 0.0391

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.0409 Hom.: 71

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

Submissions by phenotype

not provided Benign:2

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
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_noAF	Benign	-0.60
Cadd	Benign	3.5
Dann	Benign	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

Other links and lift over

dbSNP: rs368356511; hg19: chrX-153455598; COSMIC: COSV64039735;