7-128772646-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001385125.1(OPN1SW):āc.932T>Cā(p.Ile311Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I311N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001385125.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1SW | NM_001385125.1 | c.932T>C | p.Ile311Thr | missense_variant | 5/5 | ENST00000249389.3 | |
CALU | NM_001219.5 | c.*3479A>G | 3_prime_UTR_variant | 7/7 | ENST00000249364.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1SW | ENST00000249389.3 | c.932T>C | p.Ile311Thr | missense_variant | 5/5 | 1 | NM_001385125.1 | P1 | |
CALU | ENST00000249364.9 | c.*3479A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_001219.5 | |||
CALU | ENST00000449187.7 | c.*3479A>G | 3_prime_UTR_variant | 7/7 | 1 | P1 | |||
CALU | ENST00000542996.7 | c.*3479A>G | 3_prime_UTR_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251418Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135882
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727220
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 24, 2019 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with OPN1SW-related conditions. This variant is present in population databases (rs201497890, ExAC 0.03%). This sequence change replaces isoleucine with threonine at codon 314 of the OPN1SW protein (p.Ile314Thr). The isoleucine residue is highly conserved and there is a moderate physicochemical difference between isoleucine and threonine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at