Variant rs1356410 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_213600.4(PLA2G4F):c.2218A>G(p.Met740Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 1,613,624 control chromosomes in the GnomAD database, including 402,641 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.74 ( 42634 hom., cov: 30)

Exomes 𝑓: 0.70 ( 360007 hom. )

Consequence

PLA2G4F
NM_213600.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Variant links:

Genes affected

PLA2G4F (HGNC:27396): (phospholipase A2 group IVF) Predicted to enable calcium ion binding activity; calcium-dependent phospholipase A2 activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within several processes, including arachidonic acid secretion; cellular response to antibiotic; and prostaglandin biosynthetic process. Predicted to be located in cytoplasm. Predicted to be active in cytosol; ruffle membrane; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

PLA2G4F links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.35062E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
PLA2G4F	NM_213600.4 linkuse as main transcript	c.2218A>G	p.Met740Val	missense_variant	19/20	ENST00000397272.7	NP_998765.3
PLA2G4F	NR_033151.2 linkuse as main transcript	n.2232A>G		non_coding_transcript_exon_variant	18/19
PLA2G4F	XR_931785.1 linkuse as main transcript	n.2421A>G		non_coding_transcript_exon_variant	20/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4F	ENST00000397272.7 linkuse as main transcript	c.2218A>G	p.Met740Val	missense_variant	19/20	1	NM_213600.4	ENSP00000380442	P1	Q68DD2-1
PLA2G4F	ENST00000290497.11 linkuse as main transcript	c.*1962A>G		3_prime_UTR_variant, NMD_transcript_variant	18/19	1		ENSP00000290497
PLA2G4F	ENST00000562320.1 linkuse as main transcript	c.*23A>G		3_prime_UTR_variant, NMD_transcript_variant	3/4	1		ENSP00000455037
PLA2G4F	ENST00000569985.5 linkuse as main transcript	c.*1262A>G		3_prime_UTR_variant, NMD_transcript_variant	19/20	1		ENSP00000454330

Frequencies

GnomAD3 genomes

AF:

0.744

AC:

112901

AN:

151820

Hom.:

42590

Cov.:

show subpopulations

Gnomad AFR

AF:

0.845

Gnomad AMI

AF:

0.622

Gnomad AMR

AF:

0.736

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.834

Gnomad FIN

AF:

0.788

Gnomad MID

AF:

0.672

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.706

GnomAD3 exomes

AF:

0.744

AC:

187056

AN:

251312

Hom.:

70645

AF XY:

0.740

AC XY:

100467

AN XY:

135818

show subpopulations

Gnomad AFR exome

AF:

0.853

Gnomad AMR exome

AF:

0.805

Gnomad ASJ exome

AF:

0.598

Gnomad EAS exome

AF:

0.878

Gnomad SAS exome

AF:

0.828

Gnomad FIN exome

AF:

0.790

Gnomad NFE exome

AF:

0.672

Gnomad OTH exome

AF:

0.707

GnomAD4 exome

AF:

0.699

AC:

1021204

AN:

1461686

Hom.:

360007

Cov.:

AF XY:

0.701

AC XY:

509725

AN XY:

727148

show subpopulations

Gnomad4 AFR exome

AF:

0.850

Gnomad4 AMR exome

AF:

0.798

Gnomad4 ASJ exome

AF:

0.594

Gnomad4 EAS exome

AF:

0.884

Gnomad4 SAS exome

AF:

0.828

Gnomad4 FIN exome

AF:

0.783

Gnomad4 NFE exome

AF:

0.672

Gnomad4 OTH exome

AF:

0.707

GnomAD4 genome

AF:

0.744

AC:

113006

AN:

151938

Hom.:

42634

Cov.:

AF XY:

0.750

AC XY:

55660

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.844

Gnomad4 AMR

AF:

0.737

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.875

Gnomad4 SAS

AF:

0.834

Gnomad4 FIN

AF:

0.788

Gnomad4 NFE

AF:

0.671

Gnomad4 OTH

AF:

0.708

Alfa

AF:

0.680

Hom.:

91700

Bravo

AF:

0.742

TwinsUK

AF:

0.668

AC:

2478

ALSPAC

AF:

0.680

AC:

2622

ESP6500AA

AF:

0.843

AC:

3714

ESP6500EA

AF:

0.665

AC:

5720

ExAC

AF:

0.746

AC:

90509

Asia WGS

AF:

0.863

AC:

3002

AN:

3478

EpiCase

AF:

0.662

EpiControl

AF:

0.655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.061

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.0080

DANN

Benign

0.55

DEOGEN2

Benign

0.0050

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.016

LIST_S2

Benign

0.27

MetaRNN

Benign

7.4e-7

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.69

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.23

REVEL

Benign

0.021

Sift4G

Benign

0.24

Polyphen

0.0

Vest4

0.032

ClinPred

0.048

GERP RS

-9.4

Varity_R

0.080

gMVP

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over