chr3-52247719-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_144641.4(PPM1M):āc.635A>Gā(p.Gln212Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000379 in 1,583,798 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000067 ( 0 hom., cov: 32)
Exomes š: 0.000041 ( 0 hom. )
Consequence
PPM1M
NM_144641.4 missense
NM_144641.4 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 4.17
Genes affected
PPM1M (HGNC:26506): (protein phosphatase, Mg2+/Mn2+ dependent 1M) Predicted to enable manganese ion binding activity and phosphoprotein phosphatase activity. Predicted to be involved in protein dephosphorylation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPM1M | NM_144641.4 | c.635A>G | p.Gln212Arg | missense_variant | 4/10 | ENST00000323588.9 | NP_653242.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPM1M | ENST00000323588.9 | c.635A>G | p.Gln212Arg | missense_variant | 4/10 | 1 | NM_144641.4 | ENSP00000319894 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150336Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000422 AC: 1AN: 237168Hom.: 0 AF XY: 0.00000780 AC XY: 1AN XY: 128256
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GnomAD4 exome AF: 0.0000412 AC: 59AN: 1433462Hom.: 0 Cov.: 31 AF XY: 0.0000365 AC XY: 26AN XY: 711818
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GnomAD4 genome AF: 0.00000665 AC: 1AN: 150336Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73388
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2023 | The c.635A>G (p.Q212R) alteration is located in exon 4 (coding exon 4) of the PPM1M gene. This alteration results from a A to G substitution at nucleotide position 635, causing the glutamine (Q) at amino acid position 212 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
.;N
REVEL
Benign
Sift
Benign
.;T
Sift4G
Benign
T;T
Polyphen
D;P
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at