rs747411292
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_006244.4(PPP2R5B):c.482C>T(p.Ser161Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000498 in 1,607,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. S161S) has been classified as Benign.
Frequency
Consequence
NM_006244.4 missense
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.482C>T | p.Ser161Leu | missense_variant | 4/14 | ENST00000164133.7 | |
PPP2R5B | XM_047427199.1 | c.482C>T | p.Ser161Leu | missense_variant | 3/13 | ||
PPP2R5B | XM_011545132.3 | c.395C>T | p.Ser132Leu | missense_variant | 5/15 | ||
PPP2R5B | XM_047427200.1 | c.395C>T | p.Ser132Leu | missense_variant | 5/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5B | ENST00000164133.7 | c.482C>T | p.Ser161Leu | missense_variant | 4/14 | 1 | NM_006244.4 | P1 | |
PPP2R5B | ENST00000526559.5 | c.482C>T | p.Ser161Leu | missense_variant | 4/5 | 5 | |||
PPP2R5B | ENST00000532850.1 | c.224C>T | p.Ser75Leu | missense_variant | 4/5 | 3 | |||
PPP2R5B | ENST00000528530.1 | n.154C>T | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251480Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135918
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455630Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 724488
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Sep 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at