Genetic Variant PLA2G2A:p.Thr32Thr (chr1-19978469-C-G) – 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.96G>C(p.Thr32Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 1,613,622 control chromosomes in the GnomAD database, including 8,138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.078 ( 646 hom., cov: 32)

Exomes 𝑓: 0.094 ( 7492 hom. )

Consequence

PLA2G2A
NM_001395463.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.98

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=-0.81).

BP6

Variant 1-19978469-C-G is Benign according to our data. Variant chr1-19978469-C-G is described in ClinVar as [Benign]. Clinvar id is 3059119.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.98 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G2A	NM_001395463.1 link	c.96G>C	p.Thr32Thr	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.96G>C	p.Thr32Thr	synonymous_variant	Exon 3 of 5	1	NM_001395463.1	ENSP00000504762.1		P14555

Frequencies

GnomAD3 genomes

AF:

0.0778

AC:

11828

AN:

152076

Hom.:

650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0170

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0973

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0854

Gnomad OTH

AF:

0.0690

GnomAD3 exomes

AF:

0.109

AC:

27504

AN:

251184

Hom.:

1811

AF XY:

0.109

AC XY:

14777

AN XY:

135766

show subpopulations

Gnomad AFR exome

AF:

0.0161

Gnomad AMR exome

AF:

0.162

Gnomad ASJ exome

AF:

0.111

Gnomad EAS exome

AF:

0.225

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0966

Gnomad NFE exome

AF:

0.0881

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.0943

AC:

137803

AN:

1461428

Hom.:

7492

Cov.:

AF XY:

0.0947

AC XY:

68840

AN XY:

727022

show subpopulations

Gnomad4 AFR exome

AF:

0.0140

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.238

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.0932

Gnomad4 NFE exome

AF:

0.0863

Gnomad4 OTH exome

AF:

0.0954

GnomAD4 genome

AF:

0.0776

AC:

11817

AN:

152194

Hom.:

646

Cov.:

AF XY:

0.0818

AC XY:

6083

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0169

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.226

Gnomad4 SAS

AF:

0.127

Gnomad4 FIN

AF:

0.0973

Gnomad4 NFE

AF:

0.0854

Gnomad4 OTH

AF:

0.0669

Alfa

AF:

0.0827

Hom.:

153

Bravo

AF:

0.0788

Asia WGS

AF:

0.149

AC:

518

AN:

3476

EpiCase

AF:

0.0839

EpiControl

AF:

0.0887

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PLA2G2A-related disorder

Benign:1

Nov 19, 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

-0.81

CADD

Benign

0.83

DANN

Benign

0.40

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