2-159944117-A-G

Position:

• chr2-159944117-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.4144+789T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,012 control chromosomes in the GnomAD database, including 3,227 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 0.20 (3227 hom., cov: 31)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2R1	NM_007366.5	c.4144+789T>C		intron_variant		ENST00000283243.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2R1	ENST00000283243.13	c.4144+789T>C		intron_variant		1	NM_007366.5	P1
PLA2R1	ENST00000460710.2	n.95+789T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30591 AN: 151894 Hom.: 3232 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.201 AC: 30602 AN: 152012 Hom.: 3227 Cov.: 31 AF XY: 0.206 AC XY: 15294 AN XY: 74292

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.212

Alfa AF: 0.213 Hom.: 7416

Bravo AF: 0.193

Asia WGS AF: 0.282 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.77

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: rs1995950; hg19: chr2-160800628;