chrX-154190176-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000513.2(OPN1MW):c.532A>G(p.Ile178Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 0)
Failed GnomAD Quality Control
Consequence
OPN1MW
NM_000513.2 missense
NM_000513.2 missense
Scores
11
Clinical Significance
Conservation
PhyloP100: -2.27
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0038502216).
BP6
?
Variant X-154190176-A-G is Benign according to our data. Variant chrX-154190176-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3025002.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 38 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1MW | NM_000513.2 | c.532A>G | p.Ile178Val | missense_variant | 3/6 | ENST00000595290.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1MW | ENST00000595290.6 | c.532A>G | p.Ile178Val | missense_variant | 3/6 | 1 | NM_000513.2 | P1 | |
OPN1MW | ENST00000596998.2 | c.121A>G | p.Ile41Val | missense_variant | 1/4 | 5 | |||
OPN1MW | ENST00000595330.1 | n.542A>G | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 genomes
?
Cov.:
0
GnomAD3 exomes AF: 0.0181 AC: 167AN: 9233Hom.: 38 AF XY: 0.0142 AC XY: 26AN XY: 1831
GnomAD3 exomes
AF:
AC:
167
AN:
9233
Hom.:
AF XY:
AC XY:
26
AN XY:
1831
Gnomad AFR exome
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Gnomad OTH exome
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSRAC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome ? Cov.: 0
GnomAD4 genome
?
Cov.:
0
Alfa
AF:
Hom.:
ExAC
?
AF:
AC:
20
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 | Jan 01, 2024 | OPN1MW: PP2, BP4, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at