chr2-44218530-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002706.6(PPM1B):c.1127G>A(p.Ser376Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000019 in 1,580,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002706.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPM1B | NM_002706.6 | c.1127G>A | p.Ser376Asn | missense_variant | 5/6 | ENST00000282412.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPM1B | ENST00000282412.9 | c.1127G>A | p.Ser376Asn | missense_variant | 5/6 | 1 | NM_002706.6 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151940Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000882 AC: 2AN: 226802Hom.: 0 AF XY: 0.0000163 AC XY: 2AN XY: 122944
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1428730Hom.: 0 Cov.: 28 AF XY: 0.00000281 AC XY: 2AN XY: 711108
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at