rs2667033

Variant names:

• chr2-160057182-A-G
• rs2667033
• NM_007366.5:c.109+5113T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-160057182-A-G
• chr2-160057182-A-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.109+5113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,136 control chromosomes in the GnomAD database, including 48,432 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 0.79 (48432 hom., cov: 31)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 3 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]

ENSG00000299135 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007366.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2R1	NM_007366.5	MANE Select	c.109+5113T>C		intron	N/A	NP_031392.3
	PLA2R1	NM_001195641.2		c.109+5113T>C		intron	N/A	NP_001182570.1
	PLA2R1	NM_001007267.3		c.109+5113T>C		intron	N/A	NP_001007268.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2R1	ENST00000283243.13	TSL:1 MANE Select	c.109+5113T>C		intron	N/A	ENSP00000283243.7
	PLA2R1	ENST00000392771.1	TSL:1	c.109+5113T>C		intron	N/A	ENSP00000376524.1
	ENSG00000299135	ENST00000760703.1		n.165+952A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120084 AN: 152018 Hom.: 48373 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.790 AC: 120207 AN: 152136 Hom.: 48432 Cov.: 31 AF XY: 0.791 AC XY: 58772 AN XY: 74340

African (AFR) AF: 0.946 AC: 39279 AN: 41542

American (AMR) AF: 0.812 AC: 12415 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2091 AN: 3466

East Asian (EAS) AF: 0.744 AC: 3832 AN: 5152

South Asian (SAS) AF: 0.636 AC: 3063 AN: 4818

European-Finnish (FIN) AF: 0.750 AC: 7923 AN: 10562

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49349 AN: 67986

Other (OTH) AF: 0.739 AC: 1562 AN: 2114

Alfa AF: 0.733 Hom.: 22715

Bravo AF: 0.806

Asia WGS AF: 0.722 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-0.19
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: rs2667033; hg19: chr2-160913693;