chr7-128772571-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001385125.1(OPN1SW):c.1007C>T(p.Thr336Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T336T) has been classified as Likely benign.
Frequency
Consequence
NM_001385125.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1SW | NM_001385125.1 | c.1007C>T | p.Thr336Ile | missense_variant | 5/5 | ENST00000249389.3 | |
CALU | NM_001219.5 | c.*3404G>A | 3_prime_UTR_variant | 7/7 | ENST00000249364.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1SW | ENST00000249389.3 | c.1007C>T | p.Thr336Ile | missense_variant | 5/5 | 1 | NM_001385125.1 | P1 | |
CALU | ENST00000249364.9 | c.*3404G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_001219.5 | |||
CALU | ENST00000449187.7 | c.*3404G>A | 3_prime_UTR_variant | 7/7 | 1 | P1 | |||
CALU | ENST00000542996.7 | c.*3404G>A | 3_prime_UTR_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727232
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 24, 2022 | 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 852775). This variant has not been reported in the literature in individuals affected with OPN1SW-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 339 of the OPN1SW protein (p.Thr339Ile). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at