3-17009501-G-C

Position:

• chr3-17009501-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144382.2(PLCL2):​c.328-173G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,960 control chromosomes in the GnomAD database, including 28,081 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 0.60 (28081 hom., cov: 31)
• Consequence: PLCL2 NM_001144382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

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]

PLCL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLCL2	NM_001144382.2	c.328-173G>C		intron_variant		ENST00000615277.5	NP_001137854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLCL2	ENST00000615277.5	c.328-173G>C		intron_variant		1	NM_001144382.2	ENSP00000478458.1
PLCL2	ENST00000432376.5	c.-51-173G>C		intron_variant		1		ENSP00000412836.1
PLCL2	ENST00000460467.1	n.439-173G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91239 AN: 151842 Hom.: 28032 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.601 AC: 91354 AN: 151960 Hom.: 28081 Cov.: 31 AF XY: 0.605 AC XY: 44929 AN XY: 74254

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.585

Alfa AF: 0.554 Hom.: 2806

Bravo AF: 0.602

Asia WGS AF: 0.673 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.61

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: rs7612044; hg19: chr3-17050993;