rs3792161

Variant names:

• chr2-159952712-C-T
• rs3792161
• NM_007366.5:c.3302-1134G>A

Variant summary

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

The NM_007366.5(PLA2R1):​c.3302-1134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,056 control chromosomes in the GnomAD database, including 2,789 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 0.18 (2789 hom., cov: 32)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 3 publications found

Genes affected

PLA2R1 (HGNC:9042): (phospholipase A2 receptor 1) This gene represents a phospholipase A2 receptor. The encoded protein likely exists as both a transmembrane form and a soluble form. The transmembrane receptor may play a role in clearance of phospholipase A2, thereby inhibiting its action. Polymorphisms at this locus have been associated with susceptibility to idiopathic membranous nephropathy. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2R1	NM_007366.5	c.3302-1134G>A		intron_variant	Intron 23 of 29	ENST00000283243.13	NP_031392.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13	c.3302-1134G>A		intron_variant	Intron 23 of 29	1	NM_007366.5	ENSP00000283243.7
PLA2R1	ENST00000392771.1	c.3302-1134G>A		intron_variant	Intron 23 of 26	1		ENSP00000376524.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27072 AN: 151936 Hom.: 2796 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.178 AC: 27067 AN: 152056 Hom.: 2789 Cov.: 32 AF XY: 0.183 AC XY: 13624 AN XY: 74318

African (AFR) AF: 0.0876 AC: 3634 AN: 41500

American (AMR) AF: 0.173 AC: 2647 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3472

East Asian (EAS) AF: 0.181 AC: 935 AN: 5168

South Asian (SAS) AF: 0.420 AC: 2020 AN: 4808

European-Finnish (FIN) AF: 0.202 AC: 2132 AN: 10554

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14094 AN: 67962

Other (OTH) AF: 0.196 AC: 413 AN: 2106

Alfa AF: 0.210 Hom.: 1965

Bravo AF: 0.166

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.39
PhyloP100		-0.39
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: rs3792161; hg19: chr2-160809223;