rs2667011

Positions:

• chr2-160010548-G-A
• chr2-160010548-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_007366.5(PLA2R1):​c.1664+2715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,198 control chromosomes in the GnomAD database, including 52,789 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 0.83 (52789 hom., cov: 32)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2R1	NM_007366.5	c.1664+2715C>T		intron_variant		ENST00000283243.13	NP_031392.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13	c.1664+2715C>T		intron_variant		1	NM_007366.5	ENSP00000283243	P1
PLA2R1	ENST00000392771.1	c.1664+2715C>T		intron_variant		1		ENSP00000376524

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126252 AN: 152080 Hom.: 52734 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.830 AC: 126368 AN: 152198 Hom.: 52789 Cov.: 32 AF XY: 0.827 AC XY: 61516 AN XY: 74428

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.808

Alfa AF: 0.817 Hom.: 13881

Bravo AF: 0.842

Asia WGS AF: 0.760 AC: 2642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.70

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: rs2667011; hg19: chr2-160867059;