rs10516471

chr4-101171838-G-A

Variant summary

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

The NM_000944.5(PPP3CA):c.259+24078C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,992 control chromosomes in the GnomAD database, including 17,793 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 0.44 (17793 hom., cov: 32)
• Consequence: PPP3CA NM_000944.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

PPP3CA (HGNC:9314): (protein phosphatase 3 catalytic subunit alpha) Enables several functions, including ATPase binding activity; calmodulin binding activity; and calmodulin-dependent protein phosphatase activity. Involved in several processes, including calcineurin-NFAT signaling cascade; peptidyl-serine dephosphorylation; and response to calcium ion. Located in several cellular components, including cytosol; dendritic spine; and nucleoplasm. Part of calcineurin complex. Colocalizes with cytoplasmic side of plasma membrane. Implicated in developmental and epileptic encephalopathy 91. Biomarker of focal segmental glomerulosclerosis and schizophrenia. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP3CA	NM_000944.5	c.259+24078C>T		intron_variant		ENST00000394854.8
PPP3CA	NM_001130691.2	c.259+24078C>T		intron_variant
PPP3CA	NM_001130692.2	c.259+24078C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP3CA	ENST00000394854.8	c.259+24078C>T		intron_variant		1	NM_000944.5	P3

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67221 AN: 151876 Hom.: 17795 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.442 AC: 67202 AN: 151992 Hom.: 17793 Cov.: 32 AF XY: 0.441 AC XY: 32747 AN XY: 74272

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.448

Alfa AF: 0.548 Hom.: 24182

Bravo AF: 0.406

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.32
Dann	Benign	0.92

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: rs10516471; hg19: chr4-102092995;