NM_001161748.2:c.461-11T>G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001161748.2(LIM2):c.461-11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,612,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001161748.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152078Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000732 AC: 18AN: 245764Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133212
GnomAD4 exome AF: 0.000137 AC: 200AN: 1460826Hom.: 0 Cov.: 31 AF XY: 0.000120 AC XY: 87AN XY: 726580
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152078Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74272
ClinVar
Submissions by phenotype
Cataract 19 multiple types Uncertain:1
This sequence change falls in intron 4 of the LIM2 gene. It does not directly change the encoded amino acid sequence of the LIM2 protein. This variant is present in population databases (rs201548193, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with LIM2-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at