rs3792189

Positions:

• chr2-160029361-C-A
• chr2-160029361-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007366.5(PLA2R1):​c.842-398G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,800 control chromosomes in the GnomAD database, including 21,955 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 0.52 (21955 hom., cov: 30)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2R1	NM_007366.5	c.842-398G>T		intron_variant		ENST00000283243.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2R1	ENST00000283243.13	c.842-398G>T		intron_variant		1	NM_007366.5	P1
PLA2R1	ENST00000392771.1	c.842-398G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79010 AN: 151682 Hom.: 21941 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.521 AC: 79050 AN: 151800 Hom.: 21955 Cov.: 30 AF XY: 0.517 AC XY: 38331 AN XY: 74178

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.516

Alfa AF: 0.597 Hom.: 55814

Bravo AF: 0.504

Asia WGS AF: 0.522 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs3792189; hg19: chr2-160885872;