2-198276990-C-T

Variant names:

• chr2-198276990-C-T
• rs917314
• ENST00000625084.1:n.45-78305C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625084.1(PLCL1):​n.45-78305C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151,880 control chromosomes in the GnomAD database, including 44,068 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 0.76 (44068 hom., cov: 30)
• Consequence: PLCL1 ENST00000625084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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.45-78305C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114649 AN: 151760 Hom.: 44016 Cov.: 30

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.756 AC: 114759 AN: 151880 Hom.: 44068 Cov.: 30 AF XY: 0.761 AC XY: 56506 AN XY: 74212

African (AFR) AF: 0.875 AC: 36208 AN: 41404

American (AMR) AF: 0.770 AC: 11735 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2243 AN: 3470

East Asian (EAS) AF: 0.924 AC: 4794 AN: 5186

South Asian (SAS) AF: 0.703 AC: 3375 AN: 4802

European-Finnish (FIN) AF: 0.791 AC: 8326 AN: 10522

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45873 AN: 67938

Other (OTH) AF: 0.696 AC: 1469 AN: 2110

Alfa AF: 0.616 Hom.: 1567

Bravo AF: 0.762

Asia WGS AF: 0.778 AC: 2704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.23
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs917314; hg19: chr2-199141714;