chr15-42138944-A-G

Variant names:

• chr15-42138944-A-G
• rs3825786
• NM_213600.4:c.*3040T>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.*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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 5 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 (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4F	NM_213600.4	MANE Select	c.*3040T>C		downstream_gene	N/A	NP_998765.3
	PLA2G4F	NR_033151.2		n.*90T>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4F	ENST00000397272.7	TSL:1 MANE Select	c.*3040T>C		downstream_gene	N/A	ENSP00000380442.4

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24850 AN: 151878 Hom.: 2532 Cov.: 33

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: 4 AN: 20 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 3 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.164 AC: 24881 AN: 151996 Hom.: 2536 Cov.: 33 AF XY: 0.165 AC XY: 12246 AN XY: 74318

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: 38 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7477 AN: 67964

Other (OTH) AF: 0.136 AC: 287 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.46
PhyloP100		-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3825786; hg19: chr15-42431142;