chr1-19979394-C-A

Position:

• chr1-19979394-C-A

Variant summary

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

The ENST00000482011.3(PLA2G2A):​c.-107+186G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,996 control chromosomes in the GnomAD database, including 13,194 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 0.41 (13194 hom., cov: 32)
• Consequence: PLA2G2A ENST00000482011.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G2A	NM_001395463.1	c.-107+186G>T		intron_variant		ENST00000482011.3	NP_001382392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G2A	ENST00000482011.3	c.-107+186G>T		intron_variant		1	NM_001395463.1	ENSP00000504762	P1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62572 AN: 151878 Hom.: 13193 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.412 AC: 62584 AN: 151996 Hom.: 13194 Cov.: 32 AF XY: 0.410 AC XY: 30429 AN XY: 74264

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.435

Alfa AF: 0.437 Hom.: 20079

Bravo AF: 0.413

Asia WGS AF: 0.448 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.64

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: rs3753827; hg19: chr1-20305887;