dbSNP rs1058440: PLA2R1:c.2183+72G>A (chr2-159983856-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007366.5(PLA2R1):c.2183+72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 741,284 control chromosomes in the GnomAD database, including 770 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 0.047 ( 104 hom., cov: 26)

Exomes 𝑓: 0.040 ( 666 hom. )

Consequence

PLA2R1
NM_007366.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.467

Publications

1 publications found

Variant links:

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]

PLA2R1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2R1	NM_007366.5 link	c.2183+72G>A		intron_variant	Intron 13 of 29	ENST00000283243.13	NP_031392.3	Q13018-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13 link	c.2183+72G>A		intron_variant	Intron 13 of 29	1	NM_007366.5	ENSP00000283243.7		Q13018-1
PLA2R1	ENST00000392771.1 link	c.2183+72G>A		intron_variant	Intron 13 of 26	1		ENSP00000376524.1		Q13018-2

Frequencies

GnomAD3 genomes

AF:

0.0471

AC:

4375

AN:

92902

Hom.:

104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00841

Gnomad AMI

AF:

0.119

Gnomad AMR

AF:

0.0473

Gnomad ASJ

AF:

0.0517

Gnomad EAS

AF:

0.000670

Gnomad SAS

AF:

0.0612

Gnomad FIN

AF:

0.0366

Gnomad MID

AF:

0.0165

Gnomad NFE

AF:

0.0963

Gnomad OTH

AF:

0.0472

GnomAD4 exome

AF:

0.0396

AC:

25685

AN:

648272

Hom.:

666

AF XY:

0.0401

AC XY:

13559

AN XY:

337728

show subpopulations

African (AFR)

AF:

0.00799

AC:

135

AN:

16900

American (AMR)

AF:

0.0160

AC:

427

AN:

26764

Ashkenazi Jewish (ASJ)

AF:

0.0320

AC:

507

AN:

15834

East Asian (EAS)

AF:

0.0000575

AC:

AN:

34782

South Asian (SAS)

AF:

0.0483

AC:

2189

AN:

45286

European-Finnish (FIN)

AF:

0.0189

AC:

874

AN:

46158

Middle Eastern (MID)

AF:

0.0244

AC:

AN:

2334

European-Non Finnish (NFE)

AF:

0.0474

AC:

20312

AN:

428472

Other (OTH)

AF:

0.0372

AC:

1182

AN:

31742

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1204

2407

3611

4814

6018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0470

AC:

4372

AN:

93012

Hom.:

104

Cov.:

AF XY:

0.0466

AC XY:

2111

AN XY:

45340

show subpopulations

African (AFR)

AF:

0.00838

AC:

323

AN:

38550

American (AMR)

AF:

0.0473

AC:

351

AN:

7418

Ashkenazi Jewish (ASJ)

AF:

0.0517

AC:

106

AN:

2052

East Asian (EAS)

AF:

0.000670

AC:

AN:

2984

South Asian (SAS)

AF:

0.0608

AC:

222

AN:

3654

European-Finnish (FIN)

AF:

0.0366

AC:

154

AN:

4210

Middle Eastern (MID)

AF:

0.0135

AC:

AN:

222

European-Non Finnish (NFE)

AF:

0.0963

AC:

3117

AN:

32380

Other (OTH)

AF:

0.0468

AC:

AN:

1240

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

205

411

616

822

1027

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0368

Hom.:

Bravo

AF:

0.0277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.3

(source)

DANN

Benign

0.45

PhyloP100

-0.47

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over