dbSNP rs3825786: PLA2G4F:c.*3040T>C (chr15-42138944-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_213600.4(PLA2G4F):c.*3040T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,016 control chromosomes in the GnomAD database, including 2,536 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 0.16 ( 2536 hom., cov: 33)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

PLA2G4F
NM_213600.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.495

Publications

5 publications found

Variant links:

Genes affected

PLA2G4F (HGNC:27396): (phospholipase A2 group IVF) Predicted to enable calcium ion binding activity; calcium-dependent phospholipase A2 activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within several processes, including arachidonic acid secretion; cellular response to antibiotic; and prostaglandin biosynthetic process. Predicted to be located in cytoplasm. Predicted to be active in cytosol; ruffle membrane; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

PLA2G4F links:

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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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4F	NM_213600.4 link	c.*3040T>C		downstream_gene_variant		ENST00000397272.7	NP_998765.3
PLA2G4F	NR_033151.2 link	n.*90T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4F	ENST00000397272.7 link	c.*3040T>C		downstream_gene_variant		1	NM_213600.4	ENSP00000380442.4

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24850

AN:

151878

Hom.:

2532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.0968

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.0971

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.137

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.164

AC:

24881

AN:

151996

Hom.:

2536

Cov.:

AF XY:

0.165

AC XY:

12246

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.262

AC:

10843

AN:

41416

American (AMR)

AF:

0.0966

AC:

1478

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

455

AN:

3470

East Asian (EAS)

AF:

0.296

AC:

1519

AN:

5140

South Asian (SAS)

AF:

0.338

AC:

1629

AN:

4814

European-Finnish (FIN)

AF:

0.0971

AC:

1027

AN:

10582

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.110

AC:

7477

AN:

67964

Other (OTH)

AF:

0.136

AC:

287

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1045

2090

3134

4179

5224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.129

Hom.:

6314

Bravo

AF:

0.163

Asia WGS

AF:

0.313

AC:

1085

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.0

(source)

DANN

Benign

0.46

PhyloP100

-0.49

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over