rs11573191

Variant names:

• chr1-20069922-G-A
• rs11573191
• XM_005245891.6:c.83+890G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-20069922-G-A
• chr1-20069922-G-T

Variant summary

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

The XM_005245891.6(PLA2G5):​c.83+890G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,386 control chromosomes in the GnomAD database, including 2,547 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 0.18 (2547 hom., cov: 31)
• Consequence: PLA2G5 XM_005245891.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G5	XM_005245891.6	c.83+890G>A		intron_variant	Intron 4 of 7		XP_005245948.1
PLA2G5	XM_005245892.6	c.83+890G>A		intron_variant	Intron 3 of 6		XP_005245949.1
PLA2G5	XM_011541586.4	c.83+890G>A		intron_variant	Intron 2 of 5		XP_011539888.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G5	ENST00000460175.5	n.498-372G>A		intron_variant	Intron 3 of 6	3
PLA2G5	ENST00000465698.5	n.501+890G>A		intron_variant	Intron 3 of 7	3
PLA2G5	ENST00000469069.5	n.524+890G>A		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27135 AN: 151266 Hom.: 2551 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.179 AC: 27123 AN: 151386 Hom.: 2547 Cov.: 31 AF XY: 0.180 AC XY: 13333 AN XY: 73936

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.161

Alfa AF: 0.159 Hom.: 1887

Bravo AF: 0.170

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11573191; hg19: chr1-20396415;