rs1075534

Positions:

• chr8-22516561-A-G
• chr8-22516561-A-T

Variant summary

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

The NM_005605.5(PPP3CC):​c.770+3129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,036 control chromosomes in the GnomAD database, including 17,823 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 0.48 (17823 hom., cov: 32)
• Consequence: PPP3CC NM_005605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP3CC	NM_005605.5	c.770+3129A>G		intron_variant		ENST00000240139.10	NP_005596.2
LOC124901905	XR_007060851.1	n.1965-33832T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP3CC	ENST00000240139.10	c.770+3129A>G		intron_variant		1	NM_005605.5	ENSP00000240139	P3
	ENST00000664810.1	n.94-33832T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73300 AN: 151918 Hom.: 17826 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.482 AC: 73329 AN: 152036 Hom.: 17823 Cov.: 32 AF XY: 0.483 AC XY: 35910 AN XY: 74310

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.455

Alfa AF: 0.472 Hom.: 3583

Bravo AF: 0.486

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.6
DANN	Benign	0.82

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: rs1075534; hg19: chr8-22374074;