2-198097519-G-A

Variant names:

• chr2-198097519-G-A
• rs7595412
• NM_006226.4:c.2920-3766G>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.2920-3766G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,260 control chromosomes in the GnomAD database, including 63,934 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 0.92 (63934 hom., cov: 32)
• Consequence: PLCL1 NM_006226.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006226.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL1	NM_006226.4	MANE Select	c.2920-3766G>A		intron	N/A	NP_006217.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL1	ENST00000428675.6	TSL:1 MANE Select	c.2920-3766G>A		intron	N/A	ENSP00000402861.1
	PLCL1	ENST00000487695.6	TSL:5	c.2698-3766G>A		intron	N/A	ENSP00000457588.1
	PLCL1	ENST00000435320.1	TSL:2	n.*2692-3766G>A		intron	N/A	ENSP00000410488.1

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139365 AN: 152142 Hom.: 63886 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.916 AC: 139471 AN: 152260 Hom.: 63934 Cov.: 32 AF XY: 0.917 AC XY: 68227 AN XY: 74422

African (AFR) AF: 0.944 AC: 39222 AN: 41562

American (AMR) AF: 0.920 AC: 14072 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3174 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5168

South Asian (SAS) AF: 0.957 AC: 4622 AN: 4828

European-Finnish (FIN) AF: 0.881 AC: 9333 AN: 10592

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

European-Non Finnish (NFE) AF: 0.895 AC: 60865 AN: 68026

Other (OTH) AF: 0.920 AC: 1945 AN: 2114

Alfa AF: 0.907 Hom.: 199058

Bravo AF: 0.920

Asia WGS AF: 0.975 AC: 3389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.19
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: rs7595412; hg19: chr2-198962243;