rs525380

Variant names:

• chr1-20082881-A-C
• rs525380
• NM_000929.3:c.-10-1940A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-20082881-A-C
• chr1-20082881-A-T

Variant summary

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

The NM_000929.3(PLA2G5):​c.-10-1940A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,818 control chromosomes in the GnomAD database, including 23,782 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 0.56 (23782 hom., cov: 33)
• Consequence: PLA2G5 NM_000929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G5	NM_000929.3	c.-10-1940A>C		intron_variant	Intron 1 of 4	ENST00000375108.4	NP_000920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G5	ENST00000375108.4	c.-10-1940A>C		intron_variant	Intron 1 of 4	1	NM_000929.3	ENSP00000364249.3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84165 AN: 151698 Hom.: 23737 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.555 AC: 84274 AN: 151818 Hom.: 23782 Cov.: 33 AF XY: 0.557 AC XY: 41327 AN XY: 74244

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.598

Alfa AF: 0.561 Hom.: 26191

Bravo AF: 0.555

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.63

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: rs525380; hg19: chr1-20409374;