chr14-101876836-C-T

Position:

• chr14-101876836-C-T

Variant summary

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

The NM_001352913.2(PPP2R5C):​c.460-5325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 151,520 control chromosomes in the GnomAD database, including 861 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 0.10 (861 hom., cov: 32)
• Consequence: PPP2R5C NM_001352913.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

PPP2R5C (HGNC:9311): (protein phosphatase 2 regulatory subunit B'gamma) 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 gamma isoform of the regulatory subunit B56 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2R5C	NM_001352913.2	c.460-5325C>T		intron_variant		ENST00000694906.1	NP_001339842.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2R5C	ENST00000694906.1	c.460-5325C>T		intron_variant			NM_001352913.2	ENSP00000511581	P3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15184 AN: 151408 Hom.: 860 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.00675

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.100 AC: 15191 AN: 151520 Hom.: 861 Cov.: 32 AF XY: 0.0999 AC XY: 7383 AN XY: 73928

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.0977

Gnomad4 EAS AF: 0.00677

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0994

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0982 Hom.: 1024

Bravo AF: 0.0959

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.56

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: rs1741140; hg19: chr14-102343173;