chr5-146600310-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_181675.4(PPP2R2B):c.941G>A(p.Arg314His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,556 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. R314C) has been classified as Uncertain significance.
Frequency
Consequence
NM_181675.4 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 |
---|---|---|---|---|---|---|---|
PPP2R2B | NM_181675.4 | c.941G>A | p.Arg314His | missense_variant | 8/10 | ENST00000394411.9 | |
CTB-99A3.1 | XR_007058986.1 | n.229-6659C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R2B | ENST00000394411.9 | c.941G>A | p.Arg314His | missense_variant | 8/10 | 2 | NM_181675.4 | P3 | |
ENST00000512730.1 | n.247-6659C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250908Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135570
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461522Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727074
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.950G>A (p.R317H) alteration is located in exon 7 (coding exon 7) of the PPP2R2B gene. This alteration results from a G to A substitution at nucleotide position 950, causing the arginine (R) at amino acid position 317 to be replaced by a histidine (H). 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