19-18123979-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001393504.1(MAST3):c.674C>T(p.Thr225Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 1,584,122 control chromosomes in the GnomAD database, including 495 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001393504.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAST3 | NM_001393504.1 | c.674C>T | p.Thr225Met | missense_variant | 9/28 | ENST00000687212.1 | NP_001380433.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAST3 | ENST00000687212.1 | c.674C>T | p.Thr225Met | missense_variant | 9/28 | NM_001393504.1 | ENSP00000509890.1 |
Frequencies
GnomAD3 genomes AF: 0.0184 AC: 2794AN: 152214Hom.: 83 Cov.: 32
GnomAD3 exomes AF: 0.0306 AC: 6112AN: 199496Hom.: 198 AF XY: 0.0292 AC XY: 3180AN XY: 109028
GnomAD4 exome AF: 0.0149 AC: 21319AN: 1431790Hom.: 410 Cov.: 34 AF XY: 0.0158 AC XY: 11209AN XY: 710282
GnomAD4 genome AF: 0.0184 AC: 2805AN: 152332Hom.: 85 Cov.: 32 AF XY: 0.0204 AC XY: 1520AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 20, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at