rs895941

chr3-16804708-A-Cchr3-16804708-A-G

Variant summary

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

The ENST00000460467.1(PLCL2):n.438+1620A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,986 control chromosomes in the GnomAD database, including 12,574 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 0.38 (12574 hom., cov: 32)
• Consequence: PLCL2 ENST00000460467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

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

Verdict is Benign. Variant got -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 = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLCL2	ENST00000460467.1	n.438+1620A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57184 AN: 151868 Hom.: 12540 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.377 AC: 57269 AN: 151986 Hom.: 12574 Cov.: 32 AF XY: 0.371 AC XY: 27536 AN XY: 74306

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.322

Alfa AF: 0.291 Hom.: 3969

Bravo AF: 0.393

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.91
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs895941; hg19: chr3-16846216;