rs2461490

chr8-22512602-G-Cchr8-22512602-G-T

Variant summary

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

The NM_005605.5(PPP3CC):c.631-691G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,042 control chromosomes in the GnomAD database, including 23,612 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 0.54 (23612 hom., cov: 32)
• Consequence: PPP3CC NM_005605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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]

(HGNC:):

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 = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP3CC	NM_005605.5	c.631-691G>C		intron_variant		ENST00000240139.10
LOC124901905	XR_007060851.1	n.1965-29873C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP3CC	ENST00000240139.10	c.631-691G>C		intron_variant		1	NM_005605.5	P3
	ENST00000664810.1	n.94-29873C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82671 AN: 151926 Hom.: 23570 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.544 AC: 82766 AN: 152042 Hom.: 23612 Cov.: 32 AF XY: 0.544 AC XY: 40394 AN XY: 74314

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.501

Alfa AF: 0.489 Hom.: 2314

Bravo AF: 0.559

Asia WGS AF: 0.589 AC: 2046 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	0.44
Dann	Benign	0.76

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: rs2461490; hg19: chr8-22370115;