rs1879793

Variant names:

• chr8-22456473-G-A
• rs1879793
• NM_005605.5:c.49+15015G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-22456473-G-A
• chr8-22456473-G-C
• chr8-22456473-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005605.5(PPP3CC):​c.49+15015G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,866 control chromosomes in the GnomAD database, including 20,513 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 0.51 (20513 hom., cov: 31)
• Consequence: PPP3CC NM_005605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 5 publications found

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]

PPP3CC Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP3CC	NM_005605.5	c.49+15015G>A		intron_variant	Intron 1 of 13	ENST00000240139.10	NP_005596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP3CC	ENST00000240139.10	c.49+15015G>A		intron_variant	Intron 1 of 13	1	NM_005605.5	ENSP00000240139.5

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77934 AN: 151748 Hom.: 20483 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.514 AC: 78019 AN: 151866 Hom.: 20513 Cov.: 31 AF XY: 0.513 AC XY: 38076 AN XY: 74208

African (AFR) AF: 0.613 AC: 25372 AN: 41418

American (AMR) AF: 0.510 AC: 7780 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3550 AN: 5160

South Asian (SAS) AF: 0.538 AC: 2585 AN: 4804

European-Finnish (FIN) AF: 0.431 AC: 4537 AN: 10526

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30750 AN: 67914

Other (OTH) AF: 0.480 AC: 1011 AN: 2108

Alfa AF: 0.495 Hom.: 5641

Bravo AF: 0.523

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.71
DANN	Benign	0.71
PhyloP100		-0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1879793; hg19: chr8-22313986;