rs4664308

Positions:

• chr2-160060986-A-G

Variant summary

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

The NM_007366.5(PLA2R1):​c.109+1309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,240 control chromosomes in the GnomAD database, including 8,716 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 0.30 (8716 hom., cov: 33)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2R1	NM_007366.5	c.109+1309T>C		intron_variant		ENST00000283243.13	NP_031392.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13	c.109+1309T>C		intron_variant		1	NM_007366.5	ENSP00000283243	P1
PLA2R1	ENST00000392771.1	c.109+1309T>C		intron_variant		1		ENSP00000376524

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45868 AN: 152120 Hom.: 8718 Cov.: 33

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.301 AC: 45867 AN: 152240 Hom.: 8716 Cov.: 33 AF XY: 0.305 AC XY: 22693 AN XY: 74440

Gnomad4 AFR AF: 0.0879

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.271

Alfa AF: 0.385 Hom.: 12674

Bravo AF: 0.275

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.81

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: rs4664308; hg19: chr2-160917497;