rs3977

Positions:

• chr2-198269732-C-A
• chr2-198269732-C-G

Variant summary

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

The ENST00000625084.1(PLCL1):​n.45-85563C>A 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 0.426 in 151,984 control chromosomes in the GnomAD database, including 16,416 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 0.43 (16416 hom., cov: 31)
• Consequence: PLCL1 ENST00000625084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLCL1	ENST00000625084.1	n.45-85563C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64642 AN: 151866 Hom.: 16403 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.426 AC: 64673 AN: 151984 Hom.: 16416 Cov.: 31 AF XY: 0.439 AC XY: 32588 AN XY: 74266

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.412

Alfa AF: 0.471 Hom.: 8122

Bravo AF: 0.410

Asia WGS AF: 0.659 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3977; hg19: chr2-199134456;