rs3792189

Variant names:

• chr2-160029361-C-A
• rs3792189
• NM_007366.5:c.842-398G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.91).
• 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 rank	MANE	Protein	UniProt
PLA2R1	NM_007366.5	c.842-398G>T		intron_variant	Intron 4 of 29	ENST00000283243.13	NP_031392.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13	c.842-398G>T		intron_variant	Intron 4 of 29	1	NM_007366.5	ENSP00000283243.7
PLA2R1	ENST00000392771.1	c.842-398G>T		intron_variant	Intron 4 of 26	1		ENSP00000376524.1

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

African (AFR) AF: 0.344 AC: 14242 AN: 41376

American (AMR) AF: 0.469 AC: 7149 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2869 AN: 5138

South Asian (SAS) AF: 0.413 AC: 1983 AN: 4798

European-Finnish (FIN) AF: 0.614 AC: 6475 AN: 10542

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43045 AN: 67910

Other (OTH) AF: 0.516 AC: 1091 AN: 2114

Alfa AF: 0.591 Hom.: 116476

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
PhyloP100		0.25
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: rs3792189; hg19: chr2-160885872;