rs3792192

Variant names:

• chr2-160030364-G-A
• rs3792192
• NM_007366.5:c.842-1401C>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.842-1401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,122 control chromosomes in the GnomAD database, including 11,846 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 0.35 (11846 hom., cov: 33)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2R1	NM_007366.5	c.842-1401C>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.842-1401C>T		intron_variant	Intron 4 of 29	1	NM_007366.5	ENSP00000283243.7
PLA2R1	ENST00000392771.1	c.842-1401C>T		intron_variant	Intron 4 of 26	1		ENSP00000376524.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53792 AN: 152004 Hom.: 11844 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.354 AC: 53794 AN: 152122 Hom.: 11846 Cov.: 33 AF XY: 0.354 AC XY: 26296 AN XY: 74352

African (AFR) AF: 0.102 AC: 4252 AN: 41522

American (AMR) AF: 0.335 AC: 5122 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1704 AN: 5178

South Asian (SAS) AF: 0.249 AC: 1204 AN: 4826

European-Finnish (FIN) AF: 0.521 AC: 5492 AN: 10544

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33844 AN: 67986

Other (OTH) AF: 0.346 AC: 731 AN: 2110

Alfa AF: 0.392 Hom.: 8249

Bravo AF: 0.330

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.72
PhyloP100		1.1
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: rs3792192; hg19: chr2-160886875;