ENST00000625084.1:n.44+35076C>T

Variant names:

• chr2-198184494-C-T
• rs6735486
• ENST00000625084.1:n.44+35076C>T

Variant summary

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

The ENST00000625084.1(PLCL1):​n.44+35076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,000 control chromosomes in the GnomAD database, including 10,710 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 (10710 hom., cov: 32)
• Consequence: PLCL1 ENST00000625084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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+35076C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54999 AN: 151880 Hom.: 10716 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.362 AC: 55000 AN: 152000 Hom.: 10710 Cov.: 32 AF XY: 0.360 AC XY: 26714 AN XY: 74306

African (AFR) AF: 0.208 AC: 8632 AN: 41468

American (AMR) AF: 0.345 AC: 5267 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2313 AN: 5142

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4810

European-Finnish (FIN) AF: 0.400 AC: 4231 AN: 10578

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29571 AN: 67942

Other (OTH) AF: 0.407 AC: 858 AN: 2106

Alfa AF: 0.374 Hom.: 1450

Bravo AF: 0.354

Asia WGS AF: 0.365 AC: 1270 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	2.1
DANN	Benign	0.35
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs6735486; hg19: chr2-199049218;