rs11573203

Variant names:

• chr1-20072082-TG-T
• rs11573203
• NM_000929.3:c.-11+1621delG

Your query was ambiguous. Multiple possible variants found:

• chr1-20072082-TG-T
• chr1-20072082-TG-TGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000929.3(PLA2G5):​c.-11+1621delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6287 hom., cov: 19)
• Consequence: PLA2G5 NM_000929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G5	NM_000929.3	c.-11+1621delG		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.-11+1618delG		intron_variant	Intron 1 of 4	1	NM_000929.3	ENSP00000364249.3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43394 AN: 151796 Hom.: 6285 Cov.: 19

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.286 AC: 43417 AN: 151914 Hom.: 6287 Cov.: 19 AF XY: 0.287 AC XY: 21304 AN XY: 74246

African (AFR) AF: 0.297 AC: 12279 AN: 41388

American (AMR) AF: 0.276 AC: 4212 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1825 AN: 5148

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4810

European-Finnish (FIN) AF: 0.309 AC: 3264 AN: 10552

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18640 AN: 67952

Other (OTH) AF: 0.257 AC: 543 AN: 2110

Alfa AF: 0.274 Hom.: 703

Bravo AF: 0.287

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11573203; hg19: chr1-20398575;