rs10108011

chr8-22463293-G-A

Variant summary

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

The NM_005605.5(PPP3CC):c.50-11661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,100 control chromosomes in the GnomAD database, including 31,051 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 0.63 (31051 hom., cov: 32)
• Consequence: PPP3CC NM_005605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

PPP3CC (HGNC:9316): (protein phosphatase 3 catalytic subunit gamma) Calcineurin is a calcium-dependent, calmodulin-stimulated protein phosphatase involved in the downstream regulation of dopaminergic signal transduction. Calcineurin is composed of a regulatory subunit and a catalytic subunit. The protein encoded by this gene represents one of the regulatory subunits that has been found for calcineurin. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP3CC	NM_005605.5	c.50-11661G>A		intron_variant		ENST00000240139.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP3CC	ENST00000240139.10	c.50-11661G>A		intron_variant		1	NM_005605.5	P3

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95782 AN: 151982 Hom.: 31003 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.630 AC: 95880 AN: 152100 Hom.: 31051 Cov.: 32 AF XY: 0.629 AC XY: 46775 AN XY: 74356

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.588

Alfa AF: 0.570 Hom.: 24020

Bravo AF: 0.636

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.0
Dann	Benign	0.71

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: rs10108011; hg19: chr8-22320806;