Variant chr4-101025820-CAAA-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.*42_*44del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 438,870 control chromosomes in the GnomAD database, including 6 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00058 ( 0 hom., cov: 0)

Exomes 𝑓: 0.064 ( 6 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: 1.74

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 -10 ACMG points.

BP6

Variant 4-101025820-CAAA-C is Benign according to our data. Variant chr4-101025820-CAAA-C is described in ClinVar as [Benign]. Clinvar id is 1229591.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
PPP3CA	NM_000944.5 linkuse as main transcript	c.42_44del	3_prime_UTR_variant	14/14	ENST00000394854.8	NP_000935.1
PPP3CA	NM_001130691.2 linkuse as main transcript	c.42_44del	3_prime_UTR_variant	13/13		NP_001124163.1
PPP3CA	NM_001130692.2 linkuse as main transcript	c.42_44del	3_prime_UTR_variant	12/12		NP_001124164.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP3CA	ENST00000394854.8 linkuse as main transcript	c.42_44del		3_prime_UTR_variant	14/14	1	NM_000944.5	ENSP00000378323	P3	Q08209-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

34560

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00214

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000535

Gnomad ASJ

AF:

0.000859

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0340

AC:

1445

AN:

42522

Hom.:

AF XY:

0.0339

AC XY:

765

AN XY:

22536

show subpopulations

Gnomad AFR exome

AF:

0.0321

Gnomad AMR exome

AF:

0.0830

Gnomad ASJ exome

AF:

0.0313

Gnomad EAS exome

AF:

0.0572

Gnomad SAS exome

AF:

0.0475

Gnomad FIN exome

AF:

0.00436

Gnomad NFE exome

AF:

0.0251

Gnomad OTH exome

AF:

0.0489

GnomAD4 exome

AF:

0.0638

AC:

28012

AN:

438870

Hom.:

AF XY:

0.0636

AC XY:

14434

AN XY:

227096

show subpopulations

Gnomad4 AFR exome

AF:

0.0684

Gnomad4 AMR exome

AF:

0.0383

Gnomad4 ASJ exome

AF:

0.0639

Gnomad4 EAS exome

AF:

0.0490

Gnomad4 SAS exome

AF:

0.0668

Gnomad4 FIN exome

AF:

0.0506

Gnomad4 NFE exome

AF:

0.0663

Gnomad4 OTH exome

AF:

0.0645

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000578

AC:

AN:

34596

Hom.:

Cov.:

AF XY:

0.000657

AC XY:

AN XY:

15224

show subpopulations

Gnomad4 AFR

AF:

0.00214

Gnomad4 AMR

AF:

0.000533

Gnomad4 ASJ

AF:

0.000859

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00185

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

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