22-50443888-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242898.2(PPP6R2):c.2602C>A(p.Leu868Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000656 in 1,584,532 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 Uncertain significance (★).
Frequency
Consequence
NM_001242898.2 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 | UniProt |
---|---|---|---|---|---|---|---|
PPP6R2 | NM_001242898.2 | c.2602C>A | p.Leu868Met | missense_variant | 23/24 | ENST00000612753.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP6R2 | ENST00000612753.5 | c.2602C>A | p.Leu868Met | missense_variant | 23/24 | 2 | NM_001242898.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000298 AC: 6AN: 201280Hom.: 0 AF XY: 0.0000365 AC XY: 4AN XY: 109476
GnomAD4 exome AF: 0.0000440 AC: 63AN: 1432290Hom.: 0 Cov.: 30 AF XY: 0.0000408 AC XY: 29AN XY: 710134
GnomAD4 genome ? AF: 0.000269 AC: 41AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.2602C>A (p.L868M) alteration is located in exon 23 (coding exon 21) of the PPP6R2 gene. This alteration results from a C to A substitution at nucleotide position 2602, causing the leucine (L) at amino acid position 868 to be replaced by a methionine (M). 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