chr2-198205241-T-A

Variant names:

• chr2-198205241-T-A
• rs10183584
• ENST00000625084.1:n.44+55823T>A

Variant summary

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

The ENST00000625084.1(PLCL1):​n.44+55823T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 151,396 control chromosomes in the GnomAD database, including 59,713 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 0.89 (59713 hom., cov: 28)
• Consequence: PLCL1 ENST00000625084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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+55823T>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.888 AC: 134278 AN: 151282 Hom.: 59666 Cov.: 28

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.888 AC: 134381 AN: 151396 Hom.: 59713 Cov.: 28 AF XY: 0.889 AC XY: 65663 AN XY: 73852

African (AFR) AF: 0.866 AC: 35696 AN: 41228

American (AMR) AF: 0.908 AC: 13762 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3096 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5135 AN: 5142

South Asian (SAS) AF: 0.959 AC: 4605 AN: 4804

European-Finnish (FIN) AF: 0.880 AC: 9092 AN: 10336

Middle Eastern (MID) AF: 0.962 AC: 281 AN: 292

European-Non Finnish (NFE) AF: 0.885 AC: 60124 AN: 67944

Other (OTH) AF: 0.893 AC: 1881 AN: 2106

Alfa AF: 0.878 Hom.: 6711

Bravo AF: 0.888

Asia WGS AF: 0.970 AC: 3374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs10183584; hg19: chr2-199069965;