3-16897125-G-T

Variant names:

• chr3-16897125-G-T
• rs10510468
• NM_001144382.2:c.327+11759G>T

Variant summary

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

The NM_001144382.2(PLCL2):​c.327+11759G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,104 control chromosomes in the GnomAD database, including 648 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 0.074 (648 hom., cov: 32)
• Consequence: PLCL2 NM_001144382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 5 publications found

Genes affected

PLCL2 (HGNC:9064): (phospholipase C like 2) Enables GABA receptor binding activity. Predicted to be involved in negative regulation of cold-induced thermogenesis and phosphatidylinositol-mediated signaling. Predicted to act upstream of or within several processes, including B cell activation; gamma-aminobutyric acid signaling pathway; and negative regulation of B cell receptor signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCL2	NM_001144382.2	c.327+11759G>T		intron_variant	Intron 1 of 5	ENST00000615277.5	NP_001137854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCL2	ENST00000615277.5	c.327+11759G>T		intron_variant	Intron 1 of 5	1	NM_001144382.2	ENSP00000478458.1
PLCL2	ENST00000460467.1	n.438+94037G>T		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11263 AN: 151986 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.0556

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0743 AC: 11301 AN: 152104 Hom.: 648 Cov.: 32 AF XY: 0.0721 AC XY: 5365 AN XY: 74364

African (AFR) AF: 0.155 AC: 6421 AN: 41428

American (AMR) AF: 0.0726 AC: 1109 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3466

East Asian (EAS) AF: 0.0289 AC: 150 AN: 5182

South Asian (SAS) AF: 0.0557 AC: 268 AN: 4814

European-Finnish (FIN) AF: 0.0126 AC: 134 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0412 AC: 2800 AN: 68014

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0500 Hom.: 396

Bravo AF: 0.0836

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		0.057
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10510468; hg19: chr3-16938623;