rs1808850

Variant names:

• chr2-198113937-A-G
• rs1808850
• NM_006226.4:c.3105+10001A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-198113937-A-G
• chr2-198113937-A-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.3105+10001A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 151,720 control chromosomes in the GnomAD database, including 58,182 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 0.87 (58182 hom., cov: 30)
• Consequence: PLCL1 NM_006226.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCL1	NM_006226.4	c.3105+10001A>G		intron_variant	Intron 5 of 5	ENST00000428675.6	NP_006217.3
PLCL1	XM_005246643.5	c.2883+10001A>G		intron_variant	Intron 5 of 5		XP_005246700.1
PLCL1	XM_005246644.5	c.2868+10001A>G		intron_variant	Intron 5 of 5		XP_005246701.1
PLCL1	XM_017004339.3	c.2868+10001A>G		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+10001A>G		intron_variant	Intron 5 of 5	1	NM_006226.4	ENSP00000402861.1
PLCL1	ENST00000487695.6	c.2883+10001A>G		intron_variant	Intron 5 of 5	5		ENSP00000457588.1
PLCL1	ENST00000435320.1	n.*2877+10001A>G		intron_variant	Intron 6 of 6	2		ENSP00000410488.1

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132679 AN: 151602 Hom.: 58166 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.875 AC: 132744 AN: 151720 Hom.: 58182 Cov.: 30 AF XY: 0.876 AC XY: 64954 AN XY: 74118

African (AFR) AF: 0.814 AC: 33719 AN: 41410

American (AMR) AF: 0.898 AC: 13659 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3155 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5101 AN: 5108

South Asian (SAS) AF: 0.957 AC: 4606 AN: 4812

European-Finnish (FIN) AF: 0.881 AC: 9307 AN: 10570

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60259 AN: 67836

Other (OTH) AF: 0.884 AC: 1862 AN: 2106

Alfa AF: 0.889 Hom.: 73785

Bravo AF: 0.874

Asia WGS AF: 0.962 AC: 3335 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		0.084
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: rs1808850; hg19: chr2-198978661;