rs11573203

chr1-20072082-TG-Tchr1-20072082-TG-TGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000929.3(PLA2G5):c.-11+1621del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,914 control chromosomes in the GnomAD database, including 6,287 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6287 hom., cov: 19)
• Consequence: PLA2G5 NM_000929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

PLA2G5 (HGNC:9038): (phospholipase A2 group V) This gene is a member of the secretory phospholipase A2 family. It is located in a tightly-linked cluster of secretory phospholipase A2 genes on chromosome 1. The encoded enzyme catalyzes the hydrolysis of membrane phospholipids to generate lysophospholipids and free fatty acids including arachidonic acid. It preferentially hydrolyzes linoleoyl-containing phosphatidylcholine substrates. Secretion of this enzyme is thought to induce inflammatory responses in neighboring cells. Alternatively spliced transcript variants have been found, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G5	NM_000929.3	c.-11+1621del		intron_variant		ENST00000375108.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G5	ENST00000375108.4	c.-11+1621del		intron_variant		1	NM_000929.3	P1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43394 AN: 151796 Hom.: 6285 Cov.: 19

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.286 AC: 43417 AN: 151914 Hom.: 6287 Cov.: 19 AF XY: 0.287 AC XY: 21304 AN XY: 74246

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.257

Alfa AF: 0.274 Hom.: 703

Bravo AF: 0.287

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11573203; hg19: chr1-20398575;