Genetic Variant PLA2G5:p.Gly3Gly (chr1-20084839-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000929.3(PLA2G5):c.9C>T(p.Gly3Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 1,602,812 control chromosomes in the GnomAD database, including 91,725 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6982 hom., cov: 31)

Exomes 𝑓: 0.34 ( 84743 hom. )

Consequence

PLA2G5
NM_000929.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.214

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 1-20084839-C-T is Benign according to our data. Variant chr1-20084839-C-T is described in ClinVar as [Benign]. Clinvar id is 1166519.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-20084839-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.214 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G5	NM_000929.3 link	c.9C>T	p.Gly3Gly	synonymous_variant	Exon 2 of 5	ENST00000375108.4	NP_000920.1	P39877

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G5	ENST00000375108.4 link	c.9C>T	p.Gly3Gly	synonymous_variant	Exon 2 of 5	1	NM_000929.3	ENSP00000364249.3		P39877

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43342

AN:

151736

Hom.:

6974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.298

GnomAD3 exomes

AF:

0.325

AC:

81704

AN:

251322

Hom.:

14045

AF XY:

0.334

AC XY:

45357

AN XY:

135820

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.232

Gnomad ASJ exome

AF:

0.363

Gnomad EAS exome

AF:

0.307

Gnomad SAS exome

AF:

0.339

Gnomad FIN exome

AF:

0.415

Gnomad NFE exome

AF:

0.360

Gnomad OTH exome

AF:

0.344

GnomAD4 exome

AF:

0.337

AC:

488702

AN:

1450958

Hom.:

84743

Cov.:

AF XY:

0.339

AC XY:

244731

AN XY:

722518

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.240

Gnomad4 ASJ exome

AF:

0.362

Gnomad4 EAS exome

AF:

0.316

Gnomad4 SAS exome

AF:

0.337

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.344

Gnomad4 OTH exome

AF:

0.331

GnomAD4 genome

AF:

0.286

AC:

43372

AN:

151854

Hom.:

6982

Cov.:

AF XY:

0.286

AC XY:

21260

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.276

Gnomad4 ASJ

AF:

0.360

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.323

Gnomad4 FIN

AF:

0.410

Gnomad4 NFE

AF:

0.356

Gnomad4 OTH

AF:

0.304

Alfa

AF:

0.334

Hom.:

11784

Bravo

AF:

0.267

Asia WGS

AF:

0.339

AC:

1175

AN:

3478

EpiCase

AF:

0.353

EpiControl

AF:

0.350

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

7.5

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over