ENST00000625084.1:n.44+5303A>T

Variant names:

• chr2-198154721-A-T
• rs4850823
• ENST00000625084.1:n.44+5303A>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+5303A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,218 control chromosomes in the GnomAD database, including 62,832 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 0.91 (62832 hom., cov: 32)
• Consequence: PLCL1 ENST00000625084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 3 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=-1.01).
• 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+5303A>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138160 AN: 152100 Hom.: 62794 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.908 AC: 138253 AN: 152218 Hom.: 62832 Cov.: 32 AF XY: 0.909 AC XY: 67670 AN XY: 74414

African (AFR) AF: 0.927 AC: 38501 AN: 41546

American (AMR) AF: 0.915 AC: 13990 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3176 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5176

South Asian (SAS) AF: 0.957 AC: 4612 AN: 4820

European-Finnish (FIN) AF: 0.881 AC: 9323 AN: 10586

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60476 AN: 68014

Other (OTH) AF: 0.914 AC: 1929 AN: 2110

Alfa AF: 0.871 Hom.: 3203

Bravo AF: 0.912

Asia WGS AF: 0.973 AC: 3381 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs4850823; hg19: chr2-199019445;