NM_006226.4:c.3106-2998C>T

Variant names:

• chr2-198143782-C-T
• rs11674075
• NM_006226.4:c.3106-2998C>T

Variant summary

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

The NM_006226.4(PLCL1):​c.3106-2998C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,940 control chromosomes in the GnomAD database, including 11,413 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 0.37 (11413 hom., cov: 32)
• Consequence: PLCL1 NM_006226.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCL1	NM_006226.4	c.3106-2998C>T		intron_variant	Intron 5 of 5	ENST00000428675.6	NP_006217.3
PLCL1	XM_005246643.5	c.2884-2998C>T		intron_variant	Intron 5 of 5		XP_005246700.1
PLCL1	XM_005246644.5	c.2869-2998C>T		intron_variant	Intron 5 of 5		XP_005246701.1
PLCL1	XM_017004339.3	c.2869-2998C>T		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.3106-2998C>T		intron_variant	Intron 5 of 5	1	NM_006226.4	ENSP00000402861.1
PLCL1	ENST00000487695.6	c.2884-2998C>T		intron_variant	Intron 5 of 5	5		ENSP00000457588.1
PLCL1	ENST00000435320.1	n.*2878-2998C>T		intron_variant	Intron 6 of 6	2		ENSP00000410488.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56232 AN: 151822 Hom.: 11420 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.370 AC: 56230 AN: 151940 Hom.: 11413 Cov.: 32 AF XY: 0.368 AC XY: 27302 AN XY: 74264

African (AFR) AF: 0.202 AC: 8371 AN: 41466

American (AMR) AF: 0.355 AC: 5426 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2323 AN: 5164

South Asian (SAS) AF: 0.348 AC: 1672 AN: 4804

European-Finnish (FIN) AF: 0.395 AC: 4170 AN: 10544

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30725 AN: 67912

Other (OTH) AF: 0.420 AC: 886 AN: 2112

Alfa AF: 0.430 Hom.: 64107

Bravo AF: 0.364

Asia WGS AF: 0.365 AC: 1269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.37
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: rs11674075; hg19: chr2-199008506;