rs1119850

Variant names:

• chr2-198178536-G-A
• rs1119850
• ENST00000625084.1:n.44+29118G>A

Variant summary

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

The ENST00000625084.1(PLCL1):​n.44+29118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,742 control chromosomes in the GnomAD database, including 10,661 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 0.36 (10661 hom., cov: 32)
• Consequence: PLCL1 ENST00000625084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

PLCL1 (HGNC:9063): (phospholipase C like 1 (inactive)) Predicted to enable phospholipase C 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 gamma-aminobutyric acid signaling pathway; regulation of GABAergic synaptic transmission; and regulation of peptidyl-serine phosphorylation. Predicted to be located in cytoplasm and plasma membrane. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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
PLCL1	ENST00000625084.1	n.44+29118G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54775 AN: 151624 Hom.: 10667 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.361 AC: 54776 AN: 151742 Hom.: 10661 Cov.: 32 AF XY: 0.359 AC XY: 26603 AN XY: 74134

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.407

Alfa AF: 0.403 Hom.: 2568

Bravo AF: 0.353

Asia WGS AF: 0.363 AC: 1261 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1119850; hg19: chr2-199043260;