chrX-154156506-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_020061.6(OPN1LW):c.957C>T(p.Pro319=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,201,019 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000064 ( 0 hom., 4 hem., cov: 19)
Exomes 𝑓: 0.00012 ( 0 hom. 32 hem. )
Consequence
OPN1LW
NM_020061.6 synonymous
NM_020061.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.256
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BP6
?
Variant X-154156506-C-T is Benign according to our data. Variant chrX-154156506-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1284461.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-154156506-C-T is described in Lovd as [Benign]. Variant chrX-154156506-C-T is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.256 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1LW | NM_020061.6 | c.957C>T | p.Pro319= | synonymous_variant | 5/6 | ENST00000369951.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1LW | ENST00000369951.9 | c.957C>T | p.Pro319= | synonymous_variant | 5/6 | 1 | NM_020061.6 | P1 | |
OPN1LW | ENST00000442922.1 | c.384+162C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000642 AC: 7AN: 109098Hom.: 0 Cov.: 19 AF XY: 0.000127 AC XY: 4AN XY: 31560
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GnomAD3 exomes AF: 0.0000659 AC: 12AN: 182117Hom.: 1 AF XY: 0.0000300 AC XY: 2AN XY: 66717
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GnomAD4 exome AF: 0.000118 AC: 129AN: 1091921Hom.: 0 Cov.: 32 AF XY: 0.0000895 AC XY: 32AN XY: 357585
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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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at