Genetic Variant PLA2G2A:p.Tyr44Tyr (chr1-19978433-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001395463.1(PLA2G2A):c.132C>T(p.Tyr44Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,611,986 control chromosomes in the GnomAD database, including 36,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.18 ( 2794 hom., cov: 32)

Exomes 𝑓: 0.21 ( 33985 hom. )

Consequence

PLA2G2A
NM_001395463.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.456

Variant links:

Genes affected

PLA2G2A (HGNC:9031): (phospholipase A2 group IIA) The protein encoded by this gene is a member of the phospholipase A2 family (PLA2). PLA2s constitute a diverse family of enzymes with respect to sequence, function, localization, and divalent cation requirements. This gene product belongs to group II, which contains secreted form of PLA2, an extracellular enzyme that has a low molecular mass and requires calcium ions for catalysis. It catalyzes the hydrolysis of the sn-2 fatty acid acyl ester bond of phosphoglycerides, releasing free fatty acids and lysophospholipids, and thought to participate in the regulation of the phospholipid metabolism in biomembranes. Several alternatively spliced transcript variants with different 5' UTRs have been found for this gene.[provided by RefSeq, Sep 2009]

PLA2G2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-19978433-G-A is Benign according to our data. Variant chr1-19978433-G-A is described in ClinVar as [Benign]. Clinvar id is 3056896.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.456 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G2A	NM_001395463.1 link	c.132C>T	p.Tyr44Tyr	synonymous_variant	Exon 3 of 5	ENST00000482011.3	NP_001382392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G2A	ENST00000482011.3 link	c.132C>T	p.Tyr44Tyr	synonymous_variant	Exon 3 of 5	1	NM_001395463.1	ENSP00000504762.1		P14555

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26744

AN:

152026

Hom.:

2789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.0240

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.176

AC:

43563

AN:

246998

Hom.:

4668

AF XY:

0.178

AC XY:

23964

AN XY:

134344

show subpopulations

Gnomad AFR exome

AF:

0.103

Gnomad AMR exome

AF:

0.0900

Gnomad ASJ exome

AF:

0.131

Gnomad EAS exome

AF:

0.0300

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.247

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.186

GnomAD4 exome

AF:

0.208

AC:

304039

AN:

1459840

Hom.:

33985

Cov.:

AF XY:

0.207

AC XY:

150044

AN XY:

726290

show subpopulations

Gnomad4 AFR exome

AF:

0.104

Gnomad4 AMR exome

AF:

0.0958

Gnomad4 ASJ exome

AF:

0.134

Gnomad4 EAS exome

AF:

0.0187

Gnomad4 SAS exome

AF:

0.123

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.190

GnomAD4 genome

AF:

0.176

AC:

26767

AN:

152146

Hom.:

2794

Cov.:

AF XY:

0.173

AC XY:

12894

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.0240

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.240

Gnomad4 NFE

AF:

0.236

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.198

Hom.:

4015

Bravo

AF:

0.161

Asia WGS

AF:

0.0770

AC:

267

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PLA2G2A-related disorder

Benign:1

Oct 25, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.8

DANN

Benign

0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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