Genetic Variant PLA2R1:c.2037+44A>G (chr2-159987112-T-C) – 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.2037+44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,420,604 control chromosomes in the GnomAD database, including 41,884 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 0.22 ( 4129 hom., cov: 32)

Exomes 𝑓: 0.24 ( 37755 hom. )

Consequence

PLA2R1
NM_007366.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

14 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:

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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=-0.77).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2R1	NM_007366.5 link	c.2037+44A>G		intron_variant	Intron 12 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.2037+44A>G		intron_variant	Intron 12 of 29	1	NM_007366.5	ENSP00000283243.7		Q13018-1
PLA2R1	ENST00000392771.1 link	c.2037+44A>G		intron_variant	Intron 12 of 26	1		ENSP00000376524.1		Q13018-2

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33245

AN:

151992

Hom.:

4123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.271

GnomAD2 exomes

AF:

0.256

AC:

63594

AN:

248632

AF XY:

0.250

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.463

Gnomad ASJ exome

AF:

0.349

Gnomad EAS exome

AF:

0.273

Gnomad FIN exome

AF:

0.147

Gnomad NFE exome

AF:

0.231

Gnomad OTH exome

AF:

0.254

GnomAD4 exome

AF:

0.237

AC:

300129

AN:

1268494

Hom.:

37755

Cov.:

AF XY:

0.236

AC XY:

150832

AN XY:

640314

show subpopulations

African (AFR)

AF:

0.132

AC:

3891

AN:

29412

American (AMR)

AF:

0.456

AC:

20144

AN:

44218

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

8630

AN:

24766

East Asian (EAS)

AF:

0.255

AC:

9877

AN:

38706

South Asian (SAS)

AF:

0.216

AC:

17726

AN:

82236

European-Finnish (FIN)

AF:

0.154

AC:

8180

AN:

53280

Middle Eastern (MID)

AF:

0.231

AC:

1227

AN:

5314

European-Non Finnish (NFE)

AF:

0.232

AC:

217235

AN:

936644

Other (OTH)

AF:

0.245

AC:

13219

AN:

53918

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

11734

23467

35201

46934

58668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7068

14136

21204

28272

35340

<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:

0.219

AC:

33266

AN:

152110

Hom.:

4129

Cov.:

AF XY:

0.216

AC XY:

16055

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.136

AC:

5644

AN:

41486

American (AMR)

AF:

0.380

AC:

5803

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1234

AN:

3470

East Asian (EAS)

AF:

0.276

AC:

1427

AN:

5168

South Asian (SAS)

AF:

0.212

AC:

1022

AN:

4820

European-Finnish (FIN)

AF:

0.139

AC:

1467

AN:

10592

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15695

AN:

67982

Other (OTH)

AF:

0.269

AC:

569

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1309

2617

3926

5234

6543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.242

Hom.:

1945

Bravo

AF:

0.236

Asia WGS

AF:

0.256

AC:

891

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.8

(source)

DANN

Benign

0.79

PhyloP100

0.036

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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