Variant 4-101025820-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000944.5(PPP3CA):c.*44del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.40 ( 292 hom., cov: 0)

Exomes 𝑓: 0.11 ( 224 hom. )

Failed GnomAD Quality Control

Consequence

PPP3CA
NM_000944.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0900

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-101025820-CA-C is Benign according to our data. Variant chr4-101025820-CA-C is described in ClinVar as [Benign]. Clinvar id is 1289310.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
PPP3CA	NM_000944.5 linkuse as main transcript	c.*44del	3_prime_UTR_variant	14/14	ENST00000394854.8
PPP3CA	NM_001130691.2 linkuse as main transcript	c.*44del	3_prime_UTR_variant	13/13
PPP3CA	NM_001130692.2 linkuse as main transcript	c.*44del	3_prime_UTR_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP3CA	ENST00000394854.8 linkuse as main transcript	c.*44del		3_prime_UTR_variant	14/14	1	NM_000944.5	P3	Q08209-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

13788

AN:

34454

Hom.:

292

Cov.:

FAILED QC

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.470

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.410

Gnomad EAS

AF:

0.0385

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.400

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.388

GnomAD3 exomes

AF:

0.0241

AC:

1024

AN:

42522

Hom.:

AF XY:

0.0244

AC XY:

549

AN XY:

22536

show subpopulations

Gnomad AFR exome

AF:

0.0246

Gnomad AMR exome

AF:

0.0574

Gnomad ASJ exome

AF:

0.0375

Gnomad EAS exome

AF:

0.0502

Gnomad SAS exome

AF:

0.0372

Gnomad FIN exome

AF:

0.00369

Gnomad NFE exome

AF:

0.0149

Gnomad OTH exome

AF:

0.0344

GnomAD4 exome

AF:

0.106

AC:

47001

AN:

441748

Hom.:

224

Cov.:

AF XY:

0.103

AC XY:

23616

AN XY:

228732

show subpopulations

Gnomad4 AFR exome

AF:

0.0912

Gnomad4 AMR exome

AF:

0.0372

Gnomad4 ASJ exome

AF:

0.0934

Gnomad4 EAS exome

AF:

0.0633

Gnomad4 SAS exome

AF:

0.0596

Gnomad4 FIN exome

AF:

0.0743

Gnomad4 NFE exome

AF:

0.120

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.400

AC:

13791

AN:

34490

Hom.:

292

Cov.:

AF XY:

0.387

AC XY:

5874

AN XY:

15174

show subpopulations

Gnomad4 AFR

AF:

0.361

Gnomad4 AMR

AF:

0.369

Gnomad4 ASJ

AF:

0.410

Gnomad4 EAS

AF:

0.0381

Gnomad4 SAS

AF:

0.208

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.430

Gnomad4 OTH

AF:

0.386

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over