chr2-198276990-C-T

Position:

• chr2-198276990-C-T

Variant summary

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

The ENST00000625084.1(PLCL1):​n.45-78305C>T 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 0.756 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.97).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLCL1	ENST00000625084.1	n.45-78305C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.696

Alfa AF: 0.584 Hom.: 1280

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917314; hg19: chr2-199141714;