15-42141604-A-G

Variant names:

• chr15-42141604-A-G
• rs2280248
• NM_213600.4:c.*380T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.007).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_213600.4. 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
	PLA2G4F	NM_213600.4	MANE Select	c.*380T>C		3_prime_UTR	Exon 20 of 20	NP_998765.3
	PLA2G4F	NR_033151.2		n.2944T>C		non_coding_transcript_exon	Exon 19 of 19

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4F	ENST00000397272.7	TSL:1 MANE Select	c.*380T>C		3_prime_UTR	Exon 20 of 20	ENSP00000380442.4
	PLA2G4F	ENST00000290497.11	TSL:1	n.*2674T>C		non_coding_transcript_exon	Exon 19 of 19	ENSP00000290497.7
	PLA2G4F	ENST00000562320.1	TSL:1	n.*735T>C		non_coding_transcript_exon	Exon 4 of 4	ENSP00000455037.1

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

GnomAD2 exomes AF: 0.614 AC: 79712 AN: 129874 AF XY: 0.617

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 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

African (AFR) AF: 0.687 AC: 6295 AN: 9166

American (AMR) AF: 0.669 AC: 18292 AN: 27332

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 5701 AN: 11358

East Asian (EAS) AF: 0.805 AC: 7971 AN: 9906

South Asian (SAS) AF: 0.744 AC: 44496 AN: 59846

European-Finnish (FIN) AF: 0.448 AC: 5901 AN: 13170

Middle Eastern (MID) AF: 0.590 AC: 1678 AN: 2842

European-Non Finnish (NFE) AF: 0.513 AC: 86597 AN: 168896

Other (OTH) AF: 0.563 AC: 8561 AN: 15194

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

African (AFR) AF: 0.690 AC: 28502 AN: 41284

American (AMR) AF: 0.609 AC: 9288 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3468

East Asian (EAS) AF: 0.814 AC: 4132 AN: 5076

South Asian (SAS) AF: 0.768 AC: 3656 AN: 4760

European-Finnish (FIN) AF: 0.439 AC: 4626 AN: 10530

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34809 AN: 67786

Other (OTH) AF: 0.573 AC: 1205 AN: 2104

Alfa AF: 0.553 Hom.: 7850

Bravo AF: 0.597

Asia WGS AF: 0.768 AC: 2665 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.50
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2280248; hg19: chr15-42433802;