2-160060986-A-G

Variant names:

• chr2-160060986-A-G
• rs4664308
• NM_007366.5:c.109+1309T>C

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+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
• Publications: 55 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]

LOC105373717 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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+1309T>C		intron	N/A	NP_031392.3
	PLA2R1	NM_001195641.2		c.109+1309T>C		intron	N/A	NP_001182570.1
	PLA2R1	NM_001007267.3		c.109+1309T>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+1309T>C		intron	N/A	ENSP00000283243.7
	PLA2R1	ENST00000392771.1	TSL:1	c.109+1309T>C		intron	N/A	ENSP00000376524.1

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

African (AFR) AF: 0.0879 AC: 3654 AN: 41564

American (AMR) AF: 0.280 AC: 4287 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1678 AN: 5182

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4822

European-Finnish (FIN) AF: 0.506 AC: 5366 AN: 10602

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28289 AN: 67994

Other (OTH) AF: 0.271 AC: 572 AN: 2110

Alfa AF: 0.373 Hom.: 32860

Bravo AF: 0.275

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		0.34
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: rs4664308; hg19: chr2-160917497;