4-101314212-T-A

Variant names:

• chr4-101314212-T-A
• rs2044041
• NM_000944.5:c.58+32527A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000944.5(PPP3CA):​c.58+32527A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,034 control chromosomes in the GnomAD database, including 9,104 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 0.30 (9104 hom., cov: 32)
• Consequence: PPP3CA NM_000944.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development

  Inheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
• developmental and epileptic encephalopathy 91

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• undetermined early-onset epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000944.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP3CA	NM_000944.5	MANE Select	c.58+32527A>T		intron	N/A	NP_000935.1
	PPP3CA	NM_001130691.2		c.58+32527A>T		intron	N/A	NP_001124163.1
	PPP3CA	NM_001130692.2		c.58+32527A>T		intron	N/A	NP_001124164.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP3CA	ENST00000394854.8	TSL:1 MANE Select	c.58+32527A>T		intron	N/A	ENSP00000378323.3
	PPP3CA	ENST00000394853.8	TSL:1	c.58+32527A>T		intron	N/A	ENSP00000378322.4
	PPP3CA	ENST00000323055.10	TSL:1	c.58+32527A>T		intron	N/A	ENSP00000320580.6

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46372 AN: 151916 Hom.: 9108 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.305 AC: 46351 AN: 152034 Hom.: 9104 Cov.: 32 AF XY: 0.300 AC XY: 22288 AN XY: 74282

African (AFR) AF: 0.0759 AC: 3151 AN: 41518

American (AMR) AF: 0.299 AC: 4573 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5178

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3715 AN: 10518

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29786 AN: 67942

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.362 Hom.: 1412

Bravo AF: 0.286

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.0
DANN	Benign	0.70
PhyloP100		-0.094
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2044041; hg19: chr4-102235369;