chr19-48715289-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130915.2(MAMSTR):c.398G>A(p.Gly133Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000624 in 1,442,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130915.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMSTR | NM_001130915.2 | c.398G>A | p.Gly133Glu | missense_variant | 5/10 | ENST00000318083.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMSTR | ENST00000318083.11 | c.398G>A | p.Gly133Glu | missense_variant | 5/10 | 2 | NM_001130915.2 | P2 | |
MAMSTR | ENST00000594582.1 | c.89G>A | p.Gly30Glu | missense_variant | 3/7 | 1 | |||
MAMSTR | ENST00000356751.8 | c.89G>A | p.Gly30Glu | missense_variant | 3/8 | 2 | A2 | ||
MAMSTR | ENST00000599703.1 | c.548G>A | p.Gly183Glu | missense_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.0000368 AC: 8AN: 217328Hom.: 0 AF XY: 0.0000342 AC XY: 4AN XY: 116942
GnomAD4 exome AF: 0.00000624 AC: 9AN: 1442970Hom.: 0 Cov.: 32 AF XY: 0.00000419 AC XY: 3AN XY: 715796
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 20, 2023 | The c.398G>A (p.G133E) alteration is located in exon 5 (coding exon 4) of the MAMSTR gene. This alteration results from a G to A substitution at nucleotide position 398, causing the glycine (G) at amino acid position 133 to be replaced by a glutamic acid (E). 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