Variant 2-159951564-C-T 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.3316G>A(p.Gly1106Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 1,533,322 control chromosomes in the GnomAD database, including 163,322 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 0.37 ( 12836 hom., cov: 32)

Exomes 𝑓: 0.45 ( 150486 hom. )

Consequence

PLA2R1
NM_007366.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.474

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:

PLA2R1 (HGNC:):

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=1.5104307E-5).

BP6

Variant 2-159951564-C-T is Benign according to our data. Variant chr2-159951564-C-T is described in ClinVar as [Benign]. Clinvar id is 1712437.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2R1	NM_007366.5 linkuse as main transcript	c.3316G>A	p.Gly1106Ser	missense_variant	24/30	ENST00000283243.13	NP_031392.3	Q13018-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13 linkuse as main transcript	c.3316G>A	p.Gly1106Ser	missense_variant	24/30	1	NM_007366.5	ENSP00000283243.7		Q13018-1
PLA2R1	ENST00000392771.1 linkuse as main transcript	c.3316G>A	p.Gly1106Ser	missense_variant	24/27	1		ENSP00000376524.1		Q13018-2

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55649

AN:

151944

Hom.:

12836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.288

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.367

GnomAD3 exomes

AF:

0.397

AC:

99601

AN:

250600

Hom.:

22908

AF XY:

0.398

AC XY:

53916

AN XY:

135462

show subpopulations

Gnomad AFR exome

AF:

0.0930

Gnomad AMR exome

AF:

0.301

Gnomad ASJ exome

AF:

0.302

Gnomad EAS exome

AF:

0.271

Gnomad SAS exome

AF:

0.208

Gnomad FIN exome

AF:

0.617

Gnomad NFE exome

AF:

0.507

Gnomad OTH exome

AF:

0.430

GnomAD4 exome

AF:

0.452

AC:

624656

AN:

1381260

Hom.:

150486

Cov.:

AF XY:

0.447

AC XY:

308988

AN XY:

691746

show subpopulations

Gnomad4 AFR exome

AF:

0.0830

Gnomad4 AMR exome

AF:

0.304

Gnomad4 ASJ exome

AF:

0.301

Gnomad4 EAS exome

AF:

0.306

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.613

Gnomad4 NFE exome

AF:

0.495

Gnomad4 OTH exome

AF:

0.406

GnomAD4 genome

AF:

0.366

AC:

55656

AN:

152062

Hom.:

12836

Cov.:

AF XY:

0.367

AC XY:

27290

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.346

Gnomad4 ASJ

AF:

0.309

Gnomad4 EAS

AF:

0.289

Gnomad4 SAS

AF:

0.208

Gnomad4 FIN

AF:

0.631

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.462

Hom.:

40936

Bravo

AF:

0.334

TwinsUK

AF:

0.490

AC:

1816

ALSPAC

AF:

0.518

AC:

1996

ESP6500AA

AF:

0.106

AC:

468

ESP6500EA

AF:

0.490

AC:

4216

ExAC

AF:

0.395

AC:

47957

Asia WGS

AF:

0.269

AC:

938

AN:

3478

EpiCase

AF:

0.483

EpiControl

AF:

0.477

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

0.060

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.2

DANN

Benign

0.34

DEOGEN2

Benign

0.014

T;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.15

T;T

MetaRNN

Benign

0.000015

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.46

N;N

PrimateAI

Benign

0.20

PROVEAN

Benign

0.74

N;N

REVEL

Benign

0.0010

Sift

Benign

0.81

T;T

Sift4G

Benign

0.83

T;T

Polyphen

0.0

B;B

Vest4

0.054

MPC

0.064

ClinPred

0.0040

GERP RS

-3.0

Varity_R

0.014

gMVP

0.21

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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