Variant chr4-101025820-CAA-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.*43_*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 0.08 in 440,692 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.025 ( 5 hom., cov: 0)

Exomes 𝑓: 0.080 ( 11 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: 1.56

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-CAA-C is Benign according to our data. Variant chr4-101025820-CAA-C is described in ClinVar as [Benign]. Clinvar id is 1273530.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
PPP3CA	NM_000944.5 linkuse as main transcript	c.43_44del	3_prime_UTR_variant	14/14	ENST00000394854.8
PPP3CA	NM_001130691.2 linkuse as main transcript	c.43_44del	3_prime_UTR_variant	13/13
PPP3CA	NM_001130692.2 linkuse as main transcript	c.43_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.43_44del		3_prime_UTR_variant	14/14	1	NM_000944.5	P3	Q08209-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

856

AN:

34480

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0727

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0209

Gnomad ASJ

AF:

0.00172

Gnomad EAS

AF:

0.00905

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.00585

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00715

Gnomad OTH

AF:

0.0325

GnomAD3 exomes

AF:

0.0315

AC:

1338

AN:

42522

Hom.:

AF XY:

0.0307

AC XY:

691

AN XY:

22536

show subpopulations

Gnomad AFR exome

AF:

0.0338

Gnomad AMR exome

AF:

0.0565

Gnomad ASJ exome

AF:

0.0466

Gnomad EAS exome

AF:

0.0607

Gnomad SAS exome

AF:

0.0464

Gnomad FIN exome

AF:

0.00604

Gnomad NFE exome

AF:

0.0224

Gnomad OTH exome

AF:

0.0543

GnomAD4 exome

AF:

0.0800

AC:

35238

AN:

440692

Hom.:

AF XY:

0.0783

AC XY:

17857

AN XY:

228142

show subpopulations

Gnomad4 AFR exome

AF:

0.0747

Gnomad4 AMR exome

AF:

0.0404

Gnomad4 ASJ exome

AF:

0.0810

Gnomad4 EAS exome

AF:

0.0644

Gnomad4 SAS exome

AF:

0.0666

Gnomad4 FIN exome

AF:

0.0605

Gnomad4 NFE exome

AF:

0.0857

Gnomad4 OTH exome

AF:

0.0826

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0248

AC:

857

AN:

34516

Hom.:

Cov.:

AF XY:

0.0262

AC XY:

397

AN XY:

15170

show subpopulations

Gnomad4 AFR

AF:

0.0727

Gnomad4 AMR

AF:

0.0208

Gnomad4 ASJ

AF:

0.00172

Gnomad4 EAS

AF:

0.00897

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.00585

Gnomad4 NFE

AF:

0.00714

Gnomad4 OTH

AF:

0.0323

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