chr3-108162481-TA-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018010.4(IFT57):c.1285delT(p.Tyr429IlefsTer10) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000032 in 1,595,270 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018010.4 frameshift
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 AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000167 AC: 4AN: 240116Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129544
GnomAD4 exome AF: 0.0000326 AC: 47AN: 1443066Hom.: 0 Cov.: 30 AF XY: 0.0000321 AC XY: 23AN XY: 716594
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant is present in population databases (rs747262059, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with IFT57-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. This sequence change results in a frameshift in the IFT57 gene (p.Tyr429Ilefs*10). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1 amino acid(s) of the IFT57 protein and extend the protein by 8 additional amino acid residues. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at