rs895941

Variant names:

• chr3-16804708-A-C
• rs895941
• ENST00000460467.1:n.438+1620A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-16804708-A-C
• chr3-16804708-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCL2	ENST00000460467.1	n.438+1620A>C		intron_variant	Intron 1 of 2	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;