Genetic Variant PLA2G4D:c.1574-20T>C (chr15-42071571-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178034.4(PLA2G4D):c.1574-20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 1,601,322 control chromosomes in the GnomAD database, including 467,610 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 39631 hom., cov: 30)

Exomes 𝑓: 0.77 ( 427979 hom. )

Consequence

PLA2G4D
NM_178034.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

12 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4D	NM_178034.4 link	c.1574-20T>C		intron_variant	Intron 15 of 19	ENST00000290472.4	NP_828848.3	Q86XP0-1
PLA2G4D	XM_047432399.1 link	c.1574-20T>C		intron_variant	Intron 15 of 19		XP_047288355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4D	ENST00000290472.4 link	c.1574-20T>C		intron_variant	Intron 15 of 19	1	NM_178034.4	ENSP00000290472.3		Q86XP0-1
PLA2G4D	ENST00000560932.1 link	n.106-20T>C		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108613

AN:

151824

Hom.:

39607

Cov.:

show subpopulations

Gnomad AFR

AF:

0.570

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.788

Gnomad ASJ

AF:

0.801

Gnomad EAS

AF:

0.597

Gnomad SAS

AF:

0.635

Gnomad FIN

AF:

0.794

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.784

Gnomad OTH

AF:

0.747

GnomAD2 exomes

AF:

0.741

AC:

182530

AN:

246344

AF XY:

0.739

show subpopulations

Gnomad AFR exome

AF:

0.569

Gnomad AMR exome

AF:

0.790

Gnomad ASJ exome

AF:

0.796

Gnomad EAS exome

AF:

0.590

Gnomad FIN exome

AF:

0.785

Gnomad NFE exome

AF:

0.788

Gnomad OTH exome

AF:

0.762

GnomAD4 exome

AF:

0.766

AC:

1110550

AN:

1449380

Hom.:

427979

Cov.:

AF XY:

0.763

AC XY:

550399

AN XY:

721336

show subpopulations

African (AFR)

AF:

0.568

AC:

18849

AN:

33172

American (AMR)

AF:

0.792

AC:

34861

AN:

44032

Ashkenazi Jewish (ASJ)

AF:

0.798

AC:

20470

AN:

25662

East Asian (EAS)

AF:

0.616

AC:

24382

AN:

39612

South Asian (SAS)

AF:

0.639

AC:

54410

AN:

85146

European-Finnish (FIN)

AF:

0.787

AC:

41842

AN:

53200

Middle Eastern (MID)

AF:

0.746

AC:

4261

AN:

5714

European-Non Finnish (NFE)

AF:

0.785

AC:

866323

AN:

1102970

Other (OTH)

AF:

0.754

AC:

45152

AN:

59872

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

13841

27682

41523

55364

69205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.715

AC:

108691

AN:

151942

Hom.:

39631

Cov.:

AF XY:

0.717

AC XY:

53280

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.570

AC:

23586

AN:

41406

American (AMR)

AF:

0.788

AC:

12042

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.801

AC:

2780

AN:

3472

East Asian (EAS)

AF:

0.597

AC:

3064

AN:

5134

South Asian (SAS)

AF:

0.635

AC:

3056

AN:

4810

European-Finnish (FIN)

AF:

0.794

AC:

8383

AN:

10558

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.784

AC:

53267

AN:

67966

Other (OTH)

AF:

0.749

AC:

1578

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1492

2985

4477

5970

7462

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.768

Hom.:

92764

Bravo

AF:

0.709

Asia WGS

AF:

0.655

AC:

2280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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chr15-42071571-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over