Genetic Variant NM_178034.4:c.387+14T>G (chr15-42086199-A-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -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

Publications

0 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: Likely_benign. The variant received -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 VariationId is 403315.Status of the report is criteria_provided_single_submitter, 1 stars.

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.387+14T>G		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.387+14T>G		intron	N/A	ENSP00000290472.3	Q86XP0-1

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

21101

AN:

56670

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.471

AC:

27614

AN:

58584

AF XY:

0.475

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 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

African (AFR)

AF:

0.419

AC:

1293

AN:

3086

American (AMR)

AF:

0.543

AC:

5520

AN:

10166

Ashkenazi Jewish (ASJ)

AF:

0.496

AC:

2100

AN:

4232

East Asian (EAS)

AF:

0.419

AC:

1965

AN:

4692

South Asian (SAS)

AF:

0.472

AC:

12905

AN:

27350

European-Finnish (FIN)

AF:

0.476

AC:

5341

AN:

11228

Middle Eastern (MID)

AF:

0.448

AC:

248

AN:

554

European-Non Finnish (NFE)

AF:

0.388

AC:

36637

AN:

94414

Other (OTH)

AF:

0.429

AC:

3086

AN:

7188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

2618

5237

7855

10474

13092

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

284

568

852

1136

1420

<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

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

African (AFR)

AF:

0.358

AC:

5512

AN:

15386

American (AMR)

AF:

0.306

AC:

1700

AN:

5550

Ashkenazi Jewish (ASJ)

AF:

0.412

AC:

531

AN:

1288

East Asian (EAS)

AF:

0.349

AC:

441

AN:

1262

South Asian (SAS)

AF:

0.339

AC:

346

AN:

1022

European-Finnish (FIN)

AF:

0.176

AC:

537

AN:

3058

Middle Eastern (MID)

AF:

0.343

AC:

AN:

European-Non Finnish (NFE)

AF:

0.415

AC:

11589

AN:

27942

Other (OTH)

AF:

0.372

AC:

292

AN:

786

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.401

Heterozygous variant carriers

903

1806

2709

3612

4515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

236

472

708

944

1180

<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:

0.0188

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.44

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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