chr10-94328109-G-T

Variant names:

• chr10-94328109-G-T
• rs11187870
• NM_016341.4:c.*166G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016341.4(PLCE1):​c.*166G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLCE1 NM_016341.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 19 publications found

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]

NOC3L (HGNC:24034): (NOC3 like DNA replication regulator) Enables RNA binding activity. Predicted to be involved in DNA replication initiation. Predicted to act upstream of or within fat cell differentiation. Located in mitochondrion; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016341.4. 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
	PLCE1	NM_016341.4	MANE Select	c.*166G>T		3_prime_UTR	Exon 33 of 33	NP_057425.3
	PLCE1	NM_001288989.2		c.*166G>T		3_prime_UTR	Exon 33 of 33	NP_001275918.1
	PLCE1	NM_001165979.2		c.*166G>T		3_prime_UTR	Exon 32 of 32	NP_001159451.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCE1	ENST00000371380.8	TSL:1 MANE Select	c.*166G>T		3_prime_UTR	Exon 33 of 33	ENSP00000360431.2
	PLCE1	ENST00000371375.2	TSL:1	c.*3029G>T		3_prime_UTR	Exon 31 of 31	ENSP00000360426.1
	PLCE1	ENST00000675487.1		n.*3008G>T		non_coding_transcript_exon	Exon 32 of 32	ENSP00000502340.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 245674 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 138600

African (AFR) AF: 0.00 AC: 0 AN: 6718

American (AMR) AF: 0.00 AC: 0 AN: 19856

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6598

East Asian (EAS) AF: 0.00 AC: 0 AN: 8858

South Asian (SAS) AF: 0.00 AC: 0 AN: 45098

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23918

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2180

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 121482

Other (OTH) AF: 0.00 AC: 0 AN: 10966

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		1.5

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: rs11187870; hg19: chr10-96087866;