Genetic Variant PLA2G4D:c.2043+94G>C (chr15-42070623-C-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.2043+94G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 1,377,950 control chromosomes in the GnomAD database, including 450,987 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 0.80 ( 49304 hom., cov: 33)

Exomes 𝑓: 0.81 ( 401683 hom. )

Consequence

PLA2G4D
NM_178034.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.920

Publications

8 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=-0.98).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.84 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.2043+94G>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.2043+94G>C		intron	N/A	ENSP00000290472.3	Q86XP0-1
	PLA2G4D	ENST00000560932.1	TSL:1	n.669G>C		non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.804

AC:

122263

AN:

152066

Hom.:

49265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.797

Gnomad AMI

AF:

0.753

Gnomad AMR

AF:

0.852

Gnomad ASJ

AF:

0.683

Gnomad EAS

AF:

0.794

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.798

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.815

Gnomad OTH

AF:

0.806

GnomAD4 exome

AF:

0.809

AC:

991095

AN:

1225766

Hom.:

401683

Cov.:

AF XY:

0.805

AC XY:

483430

AN XY:

600670

show subpopulations

African (AFR)

AF:

0.787

AC:

21676

AN:

27556

American (AMR)

AF:

0.869

AC:

23257

AN:

26768

Ashkenazi Jewish (ASJ)

AF:

0.695

AC:

13807

AN:

19860

East Asian (EAS)

AF:

0.791

AC:

27269

AN:

34480

South Asian (SAS)

AF:

0.685

AC:

44523

AN:

65036

European-Finnish (FIN)

AF:

0.811

AC:

37082

AN:

45724

Middle Eastern (MID)

AF:

0.759

AC:

3858

AN:

5086

European-Non Finnish (NFE)

AF:

0.820

AC:

778800

AN:

949804

Other (OTH)

AF:

0.793

AC:

40823

AN:

51452

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

9028

18056

27083

36111

45139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18028

36056

54084

72112

90140

<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:

0.804

AC:

122360

AN:

152184

Hom.:

49304

Cov.:

AF XY:

0.802

AC XY:

59652

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.797

AC:

33084

AN:

41530

American (AMR)

AF:

0.852

AC:

13049

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.683

AC:

2373

AN:

3472

East Asian (EAS)

AF:

0.794

AC:

4082

AN:

5138

South Asian (SAS)

AF:

0.678

AC:

3270

AN:

4824

European-Finnish (FIN)

AF:

0.798

AC:

8459

AN:

10602

Middle Eastern (MID)

AF:

0.806

AC:

237

AN:

294

European-Non Finnish (NFE)

AF:

0.815

AC:

55417

AN:

67988

Other (OTH)

AF:

0.804

AC:

1702

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1267

2534

3801

5068

6335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

870

1740

2610

3480

4350

<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:

0.745

Hom.:

2266

Bravo

AF:

0.812

Asia WGS

AF:

0.768

AC:

2671

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.18

(source)

DANN

Benign

0.39

PhyloP100

-0.92

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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