11-111727039-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_181699.3(PPP2R1B):c.1930C>T(p.Arg644Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181699.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SIK2 | NM_015191.3 | c.*2910G>A | 3_prime_UTR_variant | 15/15 | ENST00000304987.4 | NP_056006.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP2R1B | ENST00000311129.9 | c.1930C>T | p.Arg644Cys | missense_variant | 16/16 | 1 | ENSP00000311344.5 | |||
SIK2 | ENST00000304987.4 | c.*2910G>A | 3_prime_UTR_variant | 15/15 | 1 | NM_015191.3 | ENSP00000305976.3 | |||
PPP2R1B | ENST00000530787.1 | n.62C>T | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
PPP2R1B | ENST00000426998.6 | c.1738C>T | p.Arg580Cys | missense_variant | 14/14 | 2 | ENSP00000410671.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250980Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135652
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461748Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727182
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.1930C>T (p.R644C) alteration is located in exon 16 (coding exon 16) of the PPP2R1B gene. This alteration results from a C to T substitution at nucleotide position 1930, causing the arginine (R) at amino acid position 644 to be replaced by a cysteine (C). 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