chr10-94140878-T-A

Position:

• chr10-94140878-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016341.4(PLCE1):​c.1492+8419T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,188 control chromosomes in the GnomAD database, including 36,523 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 0.66 (36523 hom., cov: 33)
• Consequence: PLCE1 NM_016341.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

Genes affected

PLCE1 (HGNC:17175): (phospholipase C epsilon 1) This gene encodes a phospholipase enzyme that catalyzes the hydrolysis of phosphatidylinositol-4,5-bisphosphate to generate two second messengers: inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). These second messengers subsequently regulate various processes affecting cell growth, differentiation, and gene expression. This enzyme is regulated by small monomeric GTPases of the Ras and Rho families and by heterotrimeric G proteins. In addition to its phospholipase C catalytic activity, this enzyme has an N-terminal domain with guanine nucleotide exchange (GEF) activity. Mutations in this gene cause early-onset nephrotic syndrome; characterized by proteinuria, edema, and diffuse mesangial sclerosis or focal and segmental glomerulosclerosis. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLCE1	NM_016341.4	c.1492+8419T>A		intron_variant		ENST00000371380.8	NP_057425.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLCE1	ENST00000371380.8	c.1492+8419T>A		intron_variant		1	NM_016341.4	ENSP00000360431	P1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100569 AN: 152070 Hom.: 36516 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.661 AC: 100594 AN: 152188 Hom.: 36523 Cov.: 33 AF XY: 0.666 AC XY: 49517 AN XY: 74402

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.698

Alfa AF: 0.734 Hom.: 5384

Bravo AF: 0.643

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	17
DANN	Benign	0.81

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

Other links and lift over

dbSNP: rs1343094; hg19: chr10-95900635;