3-49685031-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020998.4(MST1):c.1603C>T(p.Arg535Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,398,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020998.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 6AN: 214640Hom.: 0 AF XY: 0.0000257 AC XY: 3AN XY: 116736
GnomAD4 exome AF: 0.0000136 AC: 19AN: 1398886Hom.: 0 Cov.: 35 AF XY: 0.0000143 AC XY: 10AN XY: 698238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1603C>T (p.R535W) alteration is located in exon 14 (coding exon 14) of the MST1 gene. This alteration results from a C to T substitution at nucleotide position 1603, causing the arginine (R) at amino acid position 535 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at