NM_000929.3:c.-10-3409_-10-3408delTA

Variant names:

• chr1-20081410-GAT-G
• rs11573248
• NM_000929.3:c.-10-3409_-10-3408delTA

Variant summary

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

The NM_000929.3(PLA2G5):​c.-10-3409_-10-3408delTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,626 control chromosomes in the GnomAD database, including 6,212 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6212 hom., cov: 21)
• Consequence: PLA2G5 NM_000929.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000929.3. 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
	PLA2G5	NM_000929.3	MANE Select	c.-10-3409_-10-3408delTA		intron	N/A	NP_000920.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G5	ENST00000375108.4	TSL:1 MANE Select	c.-10-3410_-10-3409delAT		intron	N/A	ENSP00000364249.3
	PLA2G5	ENST00000460175.5	TSL:3	n.770-3410_770-3409delAT		intron	N/A
	PLA2G5	ENST00000465698.5	TSL:3	n.502-3410_502-3409delAT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39268 AN: 151506 Hom.: 6205 Cov.: 21

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.259 AC: 39292 AN: 151626 Hom.: 6212 Cov.: 21 AF XY: 0.254 AC XY: 18831 AN XY: 74072

African (AFR) AF: 0.110 AC: 4530 AN: 41120

American (AMR) AF: 0.225 AC: 3432 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3464

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5172

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4812

European-Finnish (FIN) AF: 0.333 AC: 3517 AN: 10546

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24505 AN: 67934

Other (OTH) AF: 0.274 AC: 578 AN: 2106

Alfa AF: 0.318 Hom.: 1040

Bravo AF: 0.242

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11573248; hg19: chr1-20407903;