rs818678

chr1-20039837-T-Cchr1-20039837-T-G

Variant summary

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

The XM_005245891.6(PLA2G5):c.-258+11128T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,020 control chromosomes in the GnomAD database, including 21,497 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 0.52 (21497 hom., cov: 32)
• Consequence: PLA2G5 XM_005245891.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G5	XM_005245891.6	c.-258+11128T>C		intron_variant
PLA2G5	XM_005245892.6	c.-139+11128T>C		intron_variant
PLA2G5	XM_005245893.6	c.-404+11128T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G5	ENST00000460175.5	n.276+11128T>C		intron_variant, non_coding_transcript_variant		3
PLA2G5	ENST00000465698.5	n.280+11128T>C		intron_variant, non_coding_transcript_variant		3
PLA2G5	ENST00000469069.5	n.184+11128T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79043 AN: 151902 Hom.: 21486 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.520 AC: 79084 AN: 152020 Hom.: 21497 Cov.: 32 AF XY: 0.515 AC XY: 38254 AN XY: 74314

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.533

Alfa AF: 0.522 Hom.: 5621

Bravo AF: 0.504

Asia WGS AF: 0.470 AC: 1634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	3.4
Dann	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs818678; hg19: chr1-20366330;