chr11-64925875-C-T

Variant names:

• chr11-64925875-C-T
• rs141617925
• NM_006244.4:c.141C>T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_006244.4(PPP2R5B):​c.141C>T​(p.Ser47Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S47S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PPP2R5B NM_006244.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

PPP2R5B (HGNC:9310): (protein phosphatase 2 regulatory subunit B'beta) The product of this gene belongs to the phosphatase 2A regulatory subunit B family. Protein phosphatase 2A 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 B56 subfamily. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BP7: Synonymous conserved (PhyloP=0.078 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R5B	NM_006244.4	c.141C>T	p.Ser47Ser	synonymous_variant	Exon 2 of 14	ENST00000164133.7	NP_006235.1
PPP2R5B	XM_047427199.1	c.141C>T	p.Ser47Ser	synonymous_variant	Exon 1 of 13		XP_047283155.1
PPP2R5B	XM_011545132.3	c.54C>T	p.Ser18Ser	synonymous_variant	Exon 3 of 15		XP_011543434.1
PPP2R5B	XM_047427200.1	c.54C>T	p.Ser18Ser	synonymous_variant	Exon 3 of 15		XP_047283156.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R5B	ENST00000164133.7	c.141C>T	p.Ser47Ser	synonymous_variant	Exon 2 of 14	1	NM_006244.4	ENSP00000164133.2
PPP2R5B	ENST00000526559.5	c.141C>T	p.Ser47Ser	synonymous_variant	Exon 2 of 5	5		ENSP00000437088.1
PPP2R5B	ENST00000532850	c.-118C>T		5_prime_UTR_variant	Exon 2 of 5	3		ENSP00000436136.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	9.7
DANN	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs141617925; hg19: chr11-64693347;