4-6415301-G-A

Position:

• chr4-6415301-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020416.4(PPP2R2C):​c.71-34207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,248 control chromosomes in the GnomAD database, including 13,369 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (13369 hom., cov: 35)
• Consequence: PPP2R2C NM_020416.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.969

Genes affected

PPP2R2C (HGNC:9306): (protein phosphatase 2 regulatory subunit Bgamma) 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 gamma isoform of the regulatory subunit B55 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP2R2C	NM_020416.4	c.71-34207C>T		intron_variant		ENST00000382599.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP2R2C	ENST00000382599.9	c.71-34207C>T		intron_variant		1	NM_020416.4	P1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62357 AN: 152130 Hom.: 13368 Cov.: 35

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.409

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.410 AC: 62384 AN: 152248 Hom.: 13369 Cov.: 35 AF XY: 0.401 AC XY: 29848 AN XY: 74448

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.406

Alfa AF: 0.465 Hom.: 33943

Bravo AF: 0.401

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs7658616; hg19: chr4-6417028;