rs1372072

Variant names:

• chr3-16913767-G-A
• rs1372072
• NM_001144382.2:c.327+28401G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-16913767-G-A
• chr3-16913767-G-C
• chr3-16913767-G-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+28401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,804 control chromosomes in the GnomAD database, including 9,431 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 0.35 (9431 hom., cov: 31)
• Consequence: PLCL2 NM_001144382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 40 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 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.327+28401G>A		intron	N/A	NP_001137854.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL2	ENST00000615277.5	TSL:1 MANE Select	c.327+28401G>A		intron	N/A	ENSP00000478458.1
	PLCL2	ENST00000460467.1	TSL:1	n.439-95907G>A		intron	N/A
	PLCL2	ENST00000955152.1		c.327+28401G>A		intron	N/A	ENSP00000625211.1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52815 AN: 151686 Hom.: 9425 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.348 AC: 52852 AN: 151804 Hom.: 9431 Cov.: 31 AF XY: 0.352 AC XY: 26140 AN XY: 74160

African (AFR) AF: 0.275 AC: 11399 AN: 41404

American (AMR) AF: 0.325 AC: 4960 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1215 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2771 AN: 5170

South Asian (SAS) AF: 0.394 AC: 1892 AN: 4806

European-Finnish (FIN) AF: 0.439 AC: 4590 AN: 10466

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24775 AN: 67918

Other (OTH) AF: 0.342 AC: 720 AN: 2108

Alfa AF: 0.356 Hom.: 33201

Bravo AF: 0.335

Asia WGS AF: 0.431 AC: 1499 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.18
PhyloP100		-0.56
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: rs1372072; hg19: chr3-16955259;