Variant rs35771982 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_007366.5(PLA2R1):c.898C>G(p.His300Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 1,603,876 control chromosomes in the GnomAD database, including 172,691 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.35 ( 11813 hom., cov: 32)

Exomes 𝑓: 0.46 ( 160878 hom. )

Consequence

PLA2R1
NM_007366.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.177

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.1223236E-4).

BP6

Variant 2-160028907-G-C is Benign according to our data. Variant chr2-160028907-G-C is described in ClinVar as [Benign]. Clinvar id is 1712438.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2R1	NM_007366.5 linkuse as main transcript	c.898C>G	p.His300Asp	missense_variant	5/30	ENST00000283243.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2R1	ENST00000283243.13 linkuse as main transcript	c.898C>G	p.His300Asp	missense_variant	5/30	1	NM_007366.5	P1	Q13018-1
PLA2R1	ENST00000392771.1 linkuse as main transcript	c.898C>G	p.His300Asp	missense_variant	5/27	1			Q13018-2

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53694

AN:

151892

Hom.:

11811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.342

GnomAD3 exomes

AF:

0.387

AC:

97175

AN:

250908

Hom.:

21008

AF XY:

0.390

AC XY:

52929

AN XY:

135578

show subpopulations

Gnomad AFR exome

AF:

0.0916

Gnomad AMR exome

AF:

0.301

Gnomad ASJ exome

AF:

0.280

Gnomad EAS exome

AF:

0.314

Gnomad SAS exome

AF:

0.242

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.492

Gnomad OTH exome

AF:

0.409

GnomAD4 exome

AF:

0.458

AC:

664970

AN:

1451864

Hom.:

160878

Cov.:

AF XY:

0.452

AC XY:

326770

AN XY:

722560

show subpopulations

Gnomad4 AFR exome

AF:

0.0841

Gnomad4 AMR exome

AF:

0.301

Gnomad4 ASJ exome

AF:

0.280

Gnomad4 EAS exome

AF:

0.362

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.506

Gnomad4 NFE exome

AF:

0.501

Gnomad4 OTH exome

AF:

0.419

GnomAD4 genome

AF:

0.353

AC:

53698

AN:

152012

Hom.:

11813

Cov.:

AF XY:

0.353

AC XY:

26226

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.335

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.520

Gnomad4 NFE

AF:

0.498

Gnomad4 OTH

AF:

0.346

Alfa

AF:

0.434

Hom.:

4925

Bravo

AF:

0.330

TwinsUK

AF:

0.487

AC:

1805

ALSPAC

AF:

0.509

AC:

1960

ESP6500AA

AF:

0.100

AC:

442

ESP6500EA

AF:

0.488

AC:

4200

ExAC

AF:

0.385

AC:

46742

Asia WGS

AF:

0.316

AC:

1100

AN:

3478

EpiCase

AF:

0.470

EpiControl

AF:

0.464

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Atypical hemolytic-uremic syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Oct 05, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.058

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.079

DANN

Benign

0.51

DEOGEN2

Benign

0.012

T;.

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.29

T;T

MetaRNN

Benign

0.00011

T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-1.0

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.29

PROVEAN

Benign

0.23

N;N

REVEL

Benign

0.0

Sift

Benign

0.63

T;T

Sift4G

Benign

0.73

T;T

Polyphen

0.0

B;B

Vest4

0.038

MPC

0.086

ClinPred

0.0059

GERP RS

-0.95

Varity_R

0.085

gMVP

0.30

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over