Variant chr1-186870529-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_024420.3(PLA2G4A):c.115+13T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00078 ( 3 hom. )

Failed GnomAD Quality Control

Consequence

PLA2G4A
NM_024420.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

PLA2G4A (HGNC:9035): (phospholipase A2 group IVA) This gene encodes a member of the cytosolic phospholipase A2 group IV family. The enzyme catalyzes the hydrolysis of membrane phospholipids to release arachidonic acid which is subsequently metabolized into eicosanoids. Eicosanoids, including prostaglandins and leukotrienes, are lipid-based cellular hormones that regulate hemodynamics, inflammatory responses, and other intracellular pathways. The hydrolysis reaction also produces lysophospholipids that are converted into platelet-activating factor. The enzyme is activated by increased intracellular Ca(2+) levels and phosphorylation, resulting in its translocation from the cytosol and nucleus to perinuclear membrane vesicles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

PLA2G4A links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 1-186870529-T-A is Benign according to our data. Variant chr1-186870529-T-A is described in ClinVar as [Benign]. Clinvar id is 1895556.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-186870529-T-A is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
PLA2G4A	NM_024420.3 linkuse as main transcript	c.115+13T>A	intron_variant	ENST00000367466.4	NP_077734.2
PLA2G4A	NM_001311193.2 linkuse as main transcript	c.115+13T>A	intron_variant		NP_001298122.2
PLA2G4A	XM_011509642.3 linkuse as main transcript	c.115+13T>A	intron_variant		XP_011507944.1
PLA2G4A	XM_047422599.1 linkuse as main transcript	c.115+13T>A	intron_variant		XP_047278555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4A	ENST00000367466.4 linkuse as main transcript	c.115+13T>A		intron_variant		1	NM_024420.3	ENSP00000356436	P1
PLA2G4A	ENST00000466600.1 linkuse as main transcript	n.184+13T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

474

AN:

141612

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00428

Gnomad AMI

AF:

0.00115

Gnomad AMR

AF:

0.00173

Gnomad ASJ

AF:

0.000598

Gnomad EAS

AF:

0.00756

Gnomad SAS

AF:

0.00436

Gnomad FIN

AF:

0.0138

Gnomad MID

AF:

0.00769

Gnomad NFE

AF:

0.00147

Gnomad OTH

AF:

0.00204

GnomAD3 exomes

AF:

0.00148

AC:

356

AN:

240500

Hom.:

AF XY:

0.00146

AC XY:

190

AN XY:

129992

show subpopulations

Gnomad AFR exome

AF:

0.000516

Gnomad AMR exome

AF:

0.000303

Gnomad ASJ exome

AF:

0.000306

Gnomad EAS exome

AF:

0.00232

Gnomad SAS exome

AF:

0.000827

Gnomad FIN exome

AF:

0.00709

Gnomad NFE exome

AF:

0.00101

Gnomad OTH exome

AF:

0.00202

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000784

AC:

1083

AN:

1381418

Hom.:

Cov.:

AF XY:

0.000735

AC XY:

508

AN XY:

691088

show subpopulations

Gnomad4 AFR exome

AF:

0.000569

Gnomad4 AMR exome

AF:

0.000477

Gnomad4 ASJ exome

AF:

0.000275

Gnomad4 EAS exome

AF:

0.000911

Gnomad4 SAS exome

AF:

0.000439

Gnomad4 FIN exome

AF:

0.00603

Gnomad4 NFE exome

AF:

0.000558

Gnomad4 OTH exome

AF:

0.00108

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00336

AC:

476

AN:

141706

Hom.:

Cov.:

AF XY:

0.00346

AC XY:

240

AN XY:

69442

show subpopulations

Gnomad4 AFR

AF:

0.00433

Gnomad4 AMR

AF:

0.00173

Gnomad4 ASJ

AF:

0.000598

Gnomad4 EAS

AF:

0.00737

Gnomad4 SAS

AF:

0.00460

Gnomad4 FIN

AF:

0.0138

Gnomad4 NFE

AF:

0.00147

Gnomad4 OTH

AF:

0.00202

Alfa

AF:

0.0112

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.20

DANN

Benign

0.61

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