3-17082892-A-G

Variant names:

• chr3-17082892-A-G
• rs4618210
• NM_001144382.2:c.3205-6841A>G

Variant summary

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

The NM_001144382.2(PLCL2):​c.3205-6841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,944 control chromosomes in the GnomAD database, including 24,668 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 0.56 (24668 hom., cov: 31)
• Consequence: PLCL2 NM_001144382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41
• Publications: 20 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144382.2. 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
	PLCL2	NM_001144382.2	MANE Select	c.3205-6841A>G		intron	N/A	NP_001137854.1
	PLCL2	NM_015184.5		c.2827-6841A>G		intron	N/A	NP_055999.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL2	ENST00000615277.5	TSL:1 MANE Select	c.3205-6841A>G		intron	N/A	ENSP00000478458.1
	PLCL2	ENST00000432376.5	TSL:1	c.2827-6841A>G		intron	N/A	ENSP00000412836.1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85141 AN: 151826 Hom.: 24622 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.561 AC: 85254 AN: 151944 Hom.: 24668 Cov.: 31 AF XY: 0.564 AC XY: 41898 AN XY: 74250

African (AFR) AF: 0.703 AC: 29105 AN: 41420

American (AMR) AF: 0.480 AC: 7336 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1690 AN: 3464

East Asian (EAS) AF: 0.615 AC: 3171 AN: 5158

South Asian (SAS) AF: 0.558 AC: 2685 AN: 4812

European-Finnish (FIN) AF: 0.625 AC: 6579 AN: 10524

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32782 AN: 67968

Other (OTH) AF: 0.531 AC: 1122 AN: 2114

Alfa AF: 0.498 Hom.: 32801

Bravo AF: 0.559

Asia WGS AF: 0.606 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.054
DANN	Benign	0.45
PhyloP100		-3.4
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: rs4618210; hg19: chr3-17124384;