19-51380545-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001161748.2(LIM2):c.420C>A(p.Tyr140*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001161748.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 38
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Cataract 19 multiple types Uncertain:1
This sequence change results in a premature translational stop signal in the LIM2 gene (p.Tyr182*). While this is not anticipated to result in nonsense mediated decay, it is expected to delete the last 34 amino acids of the LIM2 protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with LIM2-related disease. 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. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at