3-17009501-G-C

Variant names:

• chr3-17009501-G-C
• rs7612044
• NM_001144382.2:c.328-173G>C

Variant summary

Our verdict is Benign. The variant received -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
• 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 = 0.721 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.328-173G>C		intron	N/A	NP_001137854.1
	PLCL2	NM_015184.5		c.-51-173G>C		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.328-173G>C		intron	N/A	ENSP00000478458.1
	PLCL2	ENST00000432376.5	TSL:1	c.-51-173G>C		intron	N/A	ENSP00000412836.1
	PLCL2	ENST00000460467.1	TSL:1	n.439-173G>C		intron	N/A

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

African (AFR) AF: 0.728 AC: 30184 AN: 41442

American (AMR) AF: 0.571 AC: 8717 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3468

East Asian (EAS) AF: 0.638 AC: 3291 AN: 5158

South Asian (SAS) AF: 0.644 AC: 3097 AN: 4810

European-Finnish (FIN) AF: 0.638 AC: 6727 AN: 10552

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35474 AN: 67942

Other (OTH) AF: 0.585 AC: 1231 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.61
PhyloP100		-0.77
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: rs7612044; hg19: chr3-17050993;