15-59137438-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BS1_Supporting
The NM_004998.4(MYO1E):c.3269C>T(p.Thr1090Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,613,968 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_004998.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249834Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135146
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727216
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.3269C>T (p.T1090M) alteration is located in exon 28 (coding exon 28) of the MYO1E gene. This alteration results from a C to T substitution at nucleotide position 3269, causing the threonine (T) at amino acid position 1090 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 1090 of the MYO1E protein (p.Thr1090Met). 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"). This variant has not been reported in the literature in individuals affected with MYO1E-related conditions. This variant is present in population databases (rs145345597, gnomAD 0.008%). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at