chr1-19975471-G-A

Position:

• chr1-19975471-G-A

Variant summary

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

The NM_001395463.1(PLA2G2A):​c.*230C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 585,588 control chromosomes in the GnomAD database, including 4,993 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 0.099 (1010 hom., cov: 32)
  • Exomes 𝑓: 0.13 (3983 hom.)
• Consequence: PLA2G2A NM_001395463.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G2A	NM_001395463.1	c.*230C>T		3_prime_UTR_variant	5/5	ENST00000482011.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G2A	ENST00000482011.3	c.*230C>T		3_prime_UTR_variant	5/5	1	NM_001395463.1	P1

Frequencies

GnomAD3 genomes AF: 0.0992 AC: 15084 AN: 152102 Hom.: 1011 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0940

GnomAD4 exome AF: 0.128 AC: 55515 AN: 433368 Hom.: 3983 Cov.: 0 AF XY: 0.131 AC XY: 30075 AN XY: 229438

Gnomad4 AFR exome AF: 0.0230

Gnomad4 AMR exome AF: 0.195

Gnomad4 ASJ exome AF: 0.120

Gnomad4 EAS exome AF: 0.187

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.106

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.119

GnomAD4 genome AF: 0.0990 AC: 15074 AN: 152220 Hom.: 1010 Cov.: 32 AF XY: 0.104 AC XY: 7726 AN XY: 74410

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0930

Alfa AF: 0.117 Hom.: 2352

Bravo AF: 0.0996

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.53

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: rs11677; hg19: chr1-20301964;