dbSNP rs563112904: PLA2G4D:c.387+14T>G (chr15-42086199-A-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

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

The NM_178034.4(PLA2G4D):c.387+14T>G 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 0.37 ( 0 hom., cov: 0)

Exomes 𝑓: 0.42 ( 2127 hom. )

Failed GnomAD Quality Control

Consequence

PLA2G4D
NM_178034.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.436

Variant links:

Genes affected

PLA2G4D (HGNC:30038): (phospholipase A2 group IVD) The phospholipase A2 enzyme family, including PLA2G4D, catalyze the hydrolysis of glycerophospholipids at the sn-2 position and then liberate free fatty acids and lysophospholipids (Chiba et al., 2004 [PubMed 14709560]).[supplied by OMIM, Jun 2009]

PLA2G4D links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 15-42086199-A-C is Benign according to our data. Variant chr15-42086199-A-C is described in ClinVar as [Benign]. Clinvar id is 403315.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4D	NM_178034.4 link	c.387+14T>G		intron_variant	Intron 4 of 19	ENST00000290472.4	NP_828848.3	Q86XP0-1
PLA2G4D	XM_047432399.1 link	c.387+14T>G		intron_variant	Intron 4 of 19		XP_047288355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4D	ENST00000290472.4 link	c.387+14T>G		intron_variant	Intron 4 of 19	1	NM_178034.4	ENSP00000290472.3		Q86XP0-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

21101

AN:

56670

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.176

Gnomad MID

AF:

0.324

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.373

GnomAD3 exomes

AF:

0.471

AC:

27614

AN:

58584

Hom.:

552

AF XY:

0.475

AC XY:

15374

AN XY:

32392

show subpopulations

Gnomad AFR exome

AF:

0.429

Gnomad AMR exome

AF:

0.488

Gnomad ASJ exome

AF:

0.496

Gnomad EAS exome

AF:

0.408

Gnomad SAS exome

AF:

0.491

Gnomad FIN exome

AF:

0.482

Gnomad NFE exome

AF:

0.468

Gnomad OTH exome

AF:

0.470

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.424

AC:

69095

AN:

162910

Hom.:

2127

Cov.:

AF XY:

0.431

AC XY:

38297

AN XY:

88826

show subpopulations

Gnomad4 AFR exome

AF:

0.419

Gnomad4 AMR exome

AF:

0.543

Gnomad4 ASJ exome

AF:

0.496

Gnomad4 EAS exome

AF:

0.419

Gnomad4 SAS exome

AF:

0.472

Gnomad4 FIN exome

AF:

0.476

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.429

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.372

AC:

21104

AN:

56690

Hom.:

Cov.:

AF XY:

0.351

AC XY:

9251

AN XY:

26354

show subpopulations

Gnomad4 AFR

AF:

0.358

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.412

Gnomad4 EAS

AF:

0.349

Gnomad4 SAS

AF:

0.339

Gnomad4 FIN

AF:

0.176

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.372

Alfa

AF:

0.0188

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.71

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over