chr3-52249791-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144641.4(PPM1M):c.1357G>A(p.Gly453Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,330 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144641.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPM1M | NM_144641.4 | c.1357G>A | p.Gly453Ser | missense_variant | 10/10 | ENST00000323588.9 | NP_653242.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPM1M | ENST00000323588.9 | c.1357G>A | p.Gly453Ser | missense_variant | 10/10 | 1 | NM_144641.4 | ENSP00000319894 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248228Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134864
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461330Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726916
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.1357G>A (p.G453S) alteration is located in exon 10 (coding exon 10) of the PPM1M gene. This alteration results from a G to A substitution at nucleotide position 1357, causing the glycine (G) at amino acid position 453 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