chr14-60283489-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_021003.5(PPM1A):c.786T>G(p.Asp262Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D262G) has been classified as Uncertain significance.
Frequency
Consequence
NM_021003.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPM1A | NM_021003.5 | c.786T>G | p.Asp262Glu | missense_variant | 2/6 | ENST00000395076.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPM1A | ENST00000395076.9 | c.786T>G | p.Asp262Glu | missense_variant | 2/6 | 1 | NM_021003.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000488 AC: 12AN: 245908Hom.: 0 AF XY: 0.0000600 AC XY: 8AN XY: 133360
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461484Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727004
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.1005T>G (p.D335E) alteration is located in exon 2 (coding exon 2) of the PPM1A gene. This alteration results from a T to G substitution at nucleotide position 1005, causing the aspartic acid (D) at amino acid position 335 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