rs9789480

Variant names:

• chr2-198182902-C-A
• rs9789480
• ENST00000625084.1:n.44+33484C>A

Variant summary

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

The ENST00000625084.1(PLCL1):​n.44+33484C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,122 control chromosomes in the GnomAD database, including 6,424 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 0.26 (6424 hom., cov: 32)
• Consequence: PLCL1 ENST00000625084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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+33484C>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39547 AN: 152002 Hom.: 6421 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.260 AC: 39551 AN: 152122 Hom.: 6424 Cov.: 32 AF XY: 0.271 AC XY: 20150 AN XY: 74344

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.248

Alfa AF: 0.279 Hom.: 13224

Bravo AF: 0.251

Asia WGS AF: 0.450 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9789480; hg19: chr2-199047626;