5-146878727-AGCTGCTGCTGCTGCTGCTGCTGCT-AGCTGCTGCTGCT
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_181675.4(PPP2R2B):c.-273_-262del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,297,600 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00042 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00012 ( 1 hom. )
Consequence
PPP2R2B
NM_181675.4 5_prime_UTR
NM_181675.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.19
Genes affected
PPP2R2B (HGNC:9305): (protein phosphatase 2 regulatory subunit Bbeta) The product of this gene belongs to the phosphatase 2 regulatory subunit B family. Protein phosphatase 2 is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a beta isoform of the regulatory subunit B55 subfamily. Defects in this gene cause autosomal dominant spinocerebellar ataxia 12 (SCA12), a disease caused by degeneration of the cerebellum, sometimes involving the brainstem and spinal cord, and in resulting in poor coordination of speech and body movements. Multiple alternatively spliced variants, which encode different isoforms, have been identified for this gene. The 5' UTR of some of these variants includes a CAG trinucleotide repeat sequence (7-28 copies) that can be expanded to 55-78 copies in cases of SCA12. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 5-146878727-AGCTGCTGCTGCT-A is Benign according to our data. Variant chr5-146878727-AGCTGCTGCTGCT-A is described in Lovd as [Likely_benign].
BS2
High AC in GnomAd4 at 64 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP2R2B | NM_181675.4 | c.-273_-262del | 5_prime_UTR_variant | 1/10 | ENST00000394411.9 | NP_858061.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP2R2B | ENST00000394411.9 | c.-273_-262del | 5_prime_UTR_variant | 1/10 | 2 | NM_181675.4 | ENSP00000377933 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000425 AC: 64AN: 150488Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000118 AC: 135AN: 1146994Hom.: 1 AF XY: 0.0000996 AC XY: 56AN XY: 562104
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GnomAD4 genome AF: 0.000425 AC: 64AN: 150606Hom.: 0 Cov.: 0 AF XY: 0.000436 AC XY: 32AN XY: 73474
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at