3-49684119-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020998.4(MST1):āc.2087A>Gā(p.Asn696Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020998.4 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: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250892Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135652
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461336Hom.: 0 Cov.: 36 AF XY: 0.0000550 AC XY: 40AN XY: 727002
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2087A>G (p.N696S) alteration is located in exon 18 (coding exon 18) of the MST1 gene. This alteration results from a A to G substitution at nucleotide position 2087, causing the asparagine (N) at amino acid position 696 to be replaced by a serine (S). 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