chr10-86659953-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033282.4(OPN4):c.859C>T(p.Arg287Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R287Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_033282.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN4 | NM_033282.4 | c.859C>T | p.Arg287Trp | missense_variant | 6/10 | ENST00000241891.10 | |
LOC105378409 | XR_001747526.2 | n.382-1659G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN4 | ENST00000241891.10 | c.859C>T | p.Arg287Trp | missense_variant | 6/10 | 1 | NM_033282.4 | P1 | |
OPN4 | ENST00000372071.7 | c.892C>T | p.Arg298Trp | missense_variant | 7/11 | 1 | |||
OPN4 | ENST00000686083.1 | n.1558C>T | non_coding_transcript_exon_variant | 3/3 | |||||
OPN4 | ENST00000690949.1 | n.893C>T | non_coding_transcript_exon_variant | 7/11 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251082Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135796
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727226
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.892C>T (p.R298W) alteration is located in exon 7 (coding exon 7) of the OPN4 gene. This alteration results from a C to T substitution at nucleotide position 892, causing the arginine (R) at amino acid position 298 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at