15-42141604-A-T

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_213600.4(PLA2G4F):​c.*380T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.02).

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>A		3_prime_UTR	Exon 20 of 20	NP_998765.3
	PLA2G4F	NR_033151.2		n.2944T>A		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>A		3_prime_UTR	Exon 20 of 20	ENSP00000380442.4
	PLA2G4F	ENST00000290497.11	TSL:1	n.*2674T>A		non_coding_transcript_exon	Exon 19 of 19	ENSP00000290497.7
	PLA2G4F	ENST00000562320.1	TSL:1	n.*735T>A		non_coding_transcript_exon	Exon 4 of 4	ENSP00000455037.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 318362 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 180382

African (AFR) AF: 0.00 AC: 0 AN: 9226

American (AMR) AF: 0.00 AC: 0 AN: 27522

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11410

East Asian (EAS) AF: 0.00 AC: 0 AN: 9910

South Asian (SAS) AF: 0.00 AC: 0 AN: 59874

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13180

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2848

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 169154

Other (OTH) AF: 0.00 AC: 0 AN: 15238

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 7850

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.46
PhyloP100		-1.9

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;