chr5-134201788-T-G

Position:

• chr5-134201788-T-G

Variant summary

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

The ENST00000481195.6(PPP2CA):​c.486+60A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 1,541,796 control chromosomes in the GnomAD database, including 492,509 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 0.77 (45956 hom., cov: 34)
  • Exomes 𝑓: 0.80 (446553 hom.)
• Consequence: PPP2CA ENST00000481195.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

PPP2CA (HGNC:9299): (protein phosphatase 2 catalytic subunit alpha) This gene encodes the phosphatase 2A catalytic subunit. 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. This gene encodes an alpha isoform of the catalytic subunit. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2CA	NM_002715.4	c.486+60A>C		intron_variant		ENST00000481195.6	NP_002706.1
PPP2CA	NM_001355019.2	c.291+60A>C		intron_variant			NP_001341948.1
PPP2CA	NR_149151.2	n.730+60A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2CA	ENST00000481195.6	c.486+60A>C		intron_variant		1	NM_002715.4	ENSP00000418447	P4

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117589 AN: 152054 Hom.: 45931 Cov.: 34

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.758

GnomAD4 exome AF: 0.798 AC: 1109459 AN: 1389624 Hom.: 446553 AF XY: 0.797 AC XY: 551657 AN XY: 692474

Gnomad4 AFR exome AF: 0.774

Gnomad4 AMR exome AF: 0.527

Gnomad4 ASJ exome AF: 0.779

Gnomad4 EAS exome AF: 0.553

Gnomad4 SAS exome AF: 0.727

Gnomad4 FIN exome AF: 0.742

Gnomad4 NFE exome AF: 0.826

Gnomad4 OTH exome AF: 0.785

GnomAD4 genome AF: 0.773 AC: 117663 AN: 152172 Hom.: 45956 Cov.: 34 AF XY: 0.763 AC XY: 56759 AN XY: 74378

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.757

Alfa AF: 0.742 Hom.: 4639

Bravo AF: 0.763

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.68

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: rs2302599; hg19: chr5-133537479; COSMIC: COSV51537884; COSMIC: COSV51537884;