rs2280248

Positions:

• chr15-42141604-A-G
• chr15-42141604-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_213600.4(PLA2G4F):​c.*380T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 469,162 control chromosomes in the GnomAD database, including 83,299 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 0.58 (26834 hom., cov: 29)
  • Exomes 𝑓: 0.58 (56465 hom.)
• Consequence: PLA2G4F NM_213600.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G4F	NM_213600.4	c.*380T>C		3_prime_UTR_variant	20/20	ENST00000397272.7	NP_998765.3
PLA2G4F	NR_033151.2	n.2944T>C		non_coding_transcript_exon_variant	19/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4F	ENST00000397272.7	c.*380T>C		3_prime_UTR_variant	20/20	1	NM_213600.4	ENSP00000380442	P1
PLA2G4F	ENST00000290497.11	c.*2674T>C		3_prime_UTR_variant, NMD_transcript_variant	19/19	1		ENSP00000290497
PLA2G4F	ENST00000562320.1	c.*735T>C		3_prime_UTR_variant, NMD_transcript_variant	4/4	1		ENSP00000455037
PLA2G4F	ENST00000569985.5	c.*1974T>C		3_prime_UTR_variant, NMD_transcript_variant	20/20	1		ENSP00000454330

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88483 AN: 151334 Hom.: 26794 Cov.: 29

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.568

GnomAD3 exomes AF: 0.614 AC: 79712 AN: 129874 Hom.: 25560 AF XY: 0.617 AC XY: 43722 AN XY: 70896

Gnomad AFR exome AF: 0.689

Gnomad AMR exome AF: 0.670

Gnomad ASJ exome AF: 0.500

Gnomad EAS exome AF: 0.813

Gnomad SAS exome AF: 0.747

Gnomad FIN exome AF: 0.455

Gnomad NFE exome AF: 0.516

Gnomad OTH exome AF: 0.566

GnomAD4 exome AF: 0.584 AC: 185492 AN: 317710 Hom.: 56465 Cov.: 0 AF XY: 0.596 AC XY: 107307 AN XY: 180064

Gnomad4 AFR exome AF: 0.687

Gnomad4 AMR exome AF: 0.669

Gnomad4 ASJ exome AF: 0.502

Gnomad4 EAS exome AF: 0.805

Gnomad4 SAS exome AF: 0.744

Gnomad4 FIN exome AF: 0.448

Gnomad4 NFE exome AF: 0.513

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.585 AC: 88575 AN: 151452 Hom.: 26834 Cov.: 29 AF XY: 0.586 AC XY: 43386 AN XY: 73984

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.573

Alfa AF: 0.551 Hom.: 7652

Bravo AF: 0.597

Asia WGS AF: 0.768 AC: 2665 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.50

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

LitVar

Other links and lift over

dbSNP: rs2280248; hg19: chr15-42433802;