4-101257806-T-G

Position:

• chr4-101257806-T-G

Variant summary

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

The NM_000944.5(PPP3CA):​c.59-61690A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0839 in 152,182 control chromosomes in the GnomAD database, including 727 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 0.084 (727 hom., cov: 32)
• Consequence: PPP3CA NM_000944.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP3CA	NM_000944.5	c.59-61690A>C		intron_variant		ENST00000394854.8	NP_000935.1
PPP3CA	NM_001130691.2	c.59-61690A>C		intron_variant			NP_001124163.1
PPP3CA	NM_001130692.2	c.59-61690A>C		intron_variant			NP_001124164.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP3CA	ENST00000394854.8	c.59-61690A>C		intron_variant		1	NM_000944.5	ENSP00000378323	P3

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12737 AN: 152064 Hom.: 717 Cov.: 32

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0839 AC: 12764 AN: 152182 Hom.: 727 Cov.: 32 AF XY: 0.0825 AC XY: 6142 AN XY: 74426

Gnomad4 AFR AF: 0.0283

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0924 Hom.: 395

Bravo AF: 0.0826

Asia WGS AF: 0.154 AC: 533 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.35
DANN	Benign	0.59

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: rs2850965; hg19: chr4-102178963;