rs1511217

chr2-159958582-T-C

Variant summary

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

The NM_007366.5(PLA2R1):c.2905-1955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,000 control chromosomes in the GnomAD database, including 2,858 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 (2858 hom., cov: 32)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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=-0.89).
• 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/exons	MANE	UniProt
PLA2R1	NM_007366.5	c.2905-1955A>G		intron_variant		ENST00000283243.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2R1	ENST00000283243.13	c.2905-1955A>G		intron_variant		1	NM_007366.5	P1
PLA2R1	ENST00000392771.1	c.2905-1955A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27791 AN: 151880 Hom.: 2863 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.183 AC: 27794 AN: 152000 Hom.: 2858 Cov.: 32 AF XY: 0.188 AC XY: 13990 AN XY: 74320

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.198

Alfa AF: 0.212 Hom.: 4816

Bravo AF: 0.172

Asia WGS AF: 0.277 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.0
Dann	Benign	0.73

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: rs1511217; hg19: chr2-160815093;