11-64925833-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006244.4(PPP2R5B):c.99C>A(p.Arg33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,004 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 Likely benign (★).
Frequency
Consequence
NM_006244.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5B | NM_006244.4 | c.99C>A | p.Arg33= | synonymous_variant | 2/14 | ENST00000164133.7 | |
PPP2R5B | XM_047427199.1 | c.99C>A | p.Arg33= | synonymous_variant | 1/13 | ||
PPP2R5B | XM_011545132.3 | c.27-15C>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
PPP2R5B | XM_047427200.1 | c.27-15C>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5B | ENST00000164133.7 | c.99C>A | p.Arg33= | synonymous_variant | 2/14 | 1 | NM_006244.4 | P1 | |
PPP2R5B | ENST00000526559.5 | c.99C>A | p.Arg33= | synonymous_variant | 2/5 | 5 | |||
PPP2R5B | ENST00000532850.1 | c.-145-15C>A | splice_polypyrimidine_tract_variant, intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458004Hom.: 0 Cov.: 34 AF XY: 0.00000276 AC XY: 2AN XY: 725298
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.