rs11573191

Variant names:

• chr1-20069922-G-A
• rs11573191
• ENST00000460175.5:n.498-372G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460175.5(PLA2G5):​n.498-372G>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 ENST00000460175.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 5 publications found

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]

PLA2G5 Gene-Disease associations (from GenCC):

• familial benign flecked retina

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, Orphanet
• late-adult onset retinitis pigmentosa

  Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460175.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G5	ENST00000460175.5	TSL:3	n.498-372G>A		intron	N/A
	PLA2G5	ENST00000465698.5	TSL:3	n.501+890G>A		intron	N/A
	PLA2G5	ENST00000469069.5	TSL:3	n.524+890G>A		intron	N/A

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

African (AFR) AF: 0.175 AC: 7202 AN: 41184

American (AMR) AF: 0.128 AC: 1948 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1416 AN: 5120

South Asian (SAS) AF: 0.218 AC: 1032 AN: 4742

European-Finnish (FIN) AF: 0.247 AC: 2590 AN: 10492

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11903 AN: 67870

Other (OTH) AF: 0.161 AC: 337 AN: 2096

Alfa AF: 0.170 Hom.: 5457

Bravo AF: 0.170

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.044
PromoterAI		0.039	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11573191; hg19: chr1-20396415;