rs11573248

chr1-20081410-GAT-Gchr1-20081410-GAT-GATAT

Variant summary

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

The NM_000929.3(PLA2G5):c.-10-3409_-10-3408del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,626 control chromosomes in the GnomAD database, including 6,212 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6212 hom., cov: 21)
• Consequence: PLA2G5 NM_000929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

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 (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G5	NM_000929.3	c.-10-3409_-10-3408del		intron_variant		ENST00000375108.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G5	ENST00000375108.4	c.-10-3409_-10-3408del		intron_variant		1	NM_000929.3	P1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39268 AN: 151506 Hom.: 6205 Cov.: 21

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.259 AC: 39292 AN: 151626 Hom.: 6212 Cov.: 21 AF XY: 0.254 AC XY: 18831 AN XY: 74072

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.274

Alfa AF: 0.318 Hom.: 1040

Bravo AF: 0.242

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11573248; hg19: chr1-20407903;