Variant rs45625639 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000944.5(PPP3CA):c.259+25737_259+25741del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 19326 hom., cov: 0)

Consequence

PPP3CA
NM_000944.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.426

Variant links:

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]

PPP3CA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PPP3CA	NM_000944.5 linkuse as main transcript	c.259+25737_259+25741del	intron_variant	ENST00000394854.8
PPP3CA	NM_001130691.2 linkuse as main transcript	c.259+25737_259+25741del	intron_variant
PPP3CA	NM_001130692.2 linkuse as main transcript	c.259+25737_259+25741del	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP3CA	ENST00000394854.8 linkuse as main transcript	c.259+25737_259+25741del		intron_variant		1	NM_000944.5	P3	Q08209-1

Frequencies

GnomAD3 genomes

AF:

0.488

AC:

73810

AN:

151212

Hom.:

19324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.712

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.432

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.604

Gnomad OTH

AF:

0.498

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

GnomAD4 genome

AF:

0.488

AC:

73804

AN:

151328

Hom.:

19326

Cov.:

AF XY:

0.485

AC XY:

35857

AN XY:

73890

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.418

Gnomad4 ASJ

AF:

0.432

Gnomad4 EAS

AF:

0.284

Gnomad4 SAS

AF:

0.492

Gnomad4 FIN

AF:

0.629

Gnomad4 NFE

AF:

0.604

Gnomad4 OTH

AF:

0.493

Alfa

AF:

0.544

Hom.:

2842

Bravo

AF:

0.457

Asia WGS

AF:

0.392

AC:

1358

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over