rs10732279

Positions:

• chr1-19978572-C-T

Variant summary

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

The NM_001395463.1(PLA2G2A):​c.41-48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 1,610,808 control chromosomes in the GnomAD database, including 479,292 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 0.78 (46489 hom., cov: 32)
  • Exomes 𝑓: 0.77 (432803 hom.)
• Consequence: PLA2G2A NM_001395463.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

PLA2G2A (HGNC:9031): (phospholipase A2 group IIA) The protein encoded by this gene is a member of the phospholipase A2 family (PLA2). PLA2s constitute a diverse family of enzymes with respect to sequence, function, localization, and divalent cation requirements. This gene product belongs to group II, which contains secreted form of PLA2, an extracellular enzyme that has a low molecular mass and requires calcium ions for catalysis. It catalyzes the hydrolysis of the sn-2 fatty acid acyl ester bond of phosphoglycerides, releasing free fatty acids and lysophospholipids, and thought to participate in the regulation of the phospholipid metabolism in biomembranes. Several alternatively spliced transcript variants with different 5' UTRs have been found for this gene.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G2A	NM_001395463.1	c.41-48G>A		intron_variant		ENST00000482011.3	NP_001382392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G2A	ENST00000482011.3	c.41-48G>A		intron_variant		1	NM_001395463.1	ENSP00000504762	P1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118482 AN: 151978 Hom.: 46466 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.781

GnomAD3 exomes AF: 0.787 AC: 196689 AN: 249796 Hom.: 77948 AF XY: 0.790 AC XY: 106690 AN XY: 135090

Gnomad AFR exome AF: 0.804

Gnomad AMR exome AF: 0.805

Gnomad ASJ exome AF: 0.848

Gnomad EAS exome AF: 0.945

Gnomad SAS exome AF: 0.841

Gnomad FIN exome AF: 0.746

Gnomad NFE exome AF: 0.742

Gnomad OTH exome AF: 0.787

GnomAD4 exome AF: 0.769 AC: 1121699 AN: 1458712 Hom.: 432803 Cov.: 36 AF XY: 0.771 AC XY: 559424 AN XY: 725774

Gnomad4 AFR exome AF: 0.803

Gnomad4 AMR exome AF: 0.800

Gnomad4 ASJ exome AF: 0.846

Gnomad4 EAS exome AF: 0.942

Gnomad4 SAS exome AF: 0.840

Gnomad4 FIN exome AF: 0.736

Gnomad4 NFE exome AF: 0.754

Gnomad4 OTH exome AF: 0.783

GnomAD4 genome AF: 0.779 AC: 118556 AN: 152096 Hom.: 46489 Cov.: 32 AF XY: 0.783 AC XY: 58184 AN XY: 74356

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.781

Alfa AF: 0.761 Hom.: 20273

Bravo AF: 0.788

Asia WGS AF: 0.882 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.42

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: rs10732279; hg19: chr1-20305065;