rs988583

Variant names:

• chr2-198123211-C-A
• rs988583
• NM_006226.4:c.3105+19275C>A

Variant summary

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

The NM_006226.4(PLCL1):​c.3105+19275C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 152,068 control chromosomes in the GnomAD database, including 240 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 0.040 (240 hom., cov: 32)
• Consequence: PLCL1 NM_006226.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCL1	NM_006226.4	c.3105+19275C>A		intron_variant	Intron 5 of 5	ENST00000428675.6	NP_006217.3
PLCL1	XM_005246643.5	c.2883+19275C>A		intron_variant	Intron 5 of 5		XP_005246700.1
PLCL1	XM_005246644.5	c.2868+19275C>A		intron_variant	Intron 5 of 5		XP_005246701.1
PLCL1	XM_017004339.3	c.2868+19275C>A		intron_variant	Intron 5 of 5		XP_016859828.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCL1	ENST00000428675.6	c.3105+19275C>A		intron_variant	Intron 5 of 5	1	NM_006226.4	ENSP00000402861.1
PLCL1	ENST00000487695.6	c.2883+19275C>A		intron_variant	Intron 5 of 5	5		ENSP00000457588.1
PLCL1	ENST00000435320.1	n.*2877+19275C>A		intron_variant	Intron 6 of 6	2		ENSP00000410488.1

Frequencies

GnomAD3 genomes AF: 0.0395 AC: 6001 AN: 151954 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0170

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0395 AC: 6012 AN: 152068 Hom.: 240 Cov.: 32 AF XY: 0.0384 AC XY: 2857 AN XY: 74330

African (AFR) AF: 0.102 AC: 4229 AN: 41478

American (AMR) AF: 0.0192 AC: 294 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5158

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4822

European-Finnish (FIN) AF: 0.0170 AC: 180 AN: 10584

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1162 AN: 67956

Other (OTH) AF: 0.0218 AC: 46 AN: 2112

Alfa AF: 0.0249 Hom.: 236

Bravo AF: 0.0414

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs988583; hg19: chr2-198987935;