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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178034.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4D	NM_178034.4	MANE Select	c.1574-20T>C		intron	N/A	NP_828848.3	Q86XP0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4D	ENST00000290472.4	TSL:1 MANE Select	c.1574-20T>C		intron	N/A	ENSP00000290472.3	Q86XP0-1
	PLA2G4D	ENST00000560932.1	TSL:1	n.106-20T>C		intron	N/A

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

Age Distribution

Exome Het

Exome Hom

Variant carriers

20362

40724

61086

81448

101810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

822

1644

2466

3288

4110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over