3-49684742-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020998.4(MST1):c.1765G>A(p.Glu589Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000651 in 1,613,264 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250100Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135310
GnomAD4 exome AF: 0.0000664 AC: 97AN: 1461016Hom.: 0 Cov.: 40 AF XY: 0.0000482 AC XY: 35AN XY: 726830
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1765G>A (p.E589K) alteration is located in exon 15 (coding exon 15) of the MST1 gene. This alteration results from a G to A substitution at nucleotide position 1765, causing the glutamic acid (E) at amino acid position 589 to be replaced by a lysine (K). 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