chr2-197809460-C-A

Variant names:

• chr2-197809460-C-A
• rs770657
• NM_006226.4:c.240+4121C>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.240+4121C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,032 control chromosomes in the GnomAD database, including 41,411 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 0.73 (41411 hom., cov: 31)
• Consequence: PLCL1 NM_006226.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL1	NM_006226.4	MANE Select	c.240+4121C>A		intron	N/A	NP_006217.3	Q15111-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL1	ENST00000428675.6	TSL:1 MANE Select	c.240+4121C>A		intron	N/A	ENSP00000402861.1	Q15111-1
	PLCL1	ENST00000435320.1	TSL:2	n.240+4121C>A		intron	N/A	ENSP00000410488.1	F8WAR2

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110630 AN: 151914 Hom.: 41362 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.728 AC: 110734 AN: 152032 Hom.: 41411 Cov.: 31 AF XY: 0.725 AC XY: 53875 AN XY: 74288

African (AFR) AF: 0.905 AC: 37556 AN: 41512

American (AMR) AF: 0.653 AC: 9985 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2537 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2576 AN: 5148

South Asian (SAS) AF: 0.657 AC: 3157 AN: 4804

European-Finnish (FIN) AF: 0.607 AC: 6401 AN: 10542

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46055 AN: 67960

Other (OTH) AF: 0.743 AC: 1571 AN: 2114

Alfa AF: 0.699 Hom.: 19942

Bravo AF: 0.739

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.53
PhyloP100		0.42
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: rs770657; hg19: chr2-198674184;