dbSNP rs2285714: PLA2G12A:p.Glu115Glu (chr4-109717654-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_030821.5(PLA2G12A):c.345G>A(p.Glu115Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.402 in 1,613,256 control chromosomes in the GnomAD database, including 136,736 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 9095 hom., cov: 32)

Exomes 𝑓: 0.41 ( 127641 hom. )

Consequence

PLA2G12A
NM_030821.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.12

Variant links:

Genes affected

PLA2G12A (HGNC:18554): (phospholipase A2 group XIIA) Secreted phospholipase A2 (sPLA2) enzymes liberate arachidonic acid from phospholipids for production of eicosanoids and exert a variety of physiologic and pathologic effects. Group XII sPLA2s, such as PLA2G12A, have relatively low specific activity and are structurally and functionally distinct from other sPLA2s (Gelb et al., 2000 [PubMed 11031251]).[supplied by OMIM, Mar 2008]

PLA2G12A links:

ENSG00000285330 (HGNC:):

ENSG00000285330 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.2).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G12A	NM_030821.5 link	c.345G>A	p.Glu115Glu	synonymous_variant	Exon 3 of 4	ENST00000243501.10	NP_110448.2	Q9BZM1Q542Y6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G12A	ENST00000243501.10 link	c.345G>A	p.Glu115Glu	synonymous_variant	Exon 3 of 4	1	NM_030821.5	ENSP00000243501.5		Q9BZM1
ENSG00000285330	ENST00000645635.1 link	c.1671G>A	p.Glu557Glu	synonymous_variant	Exon 14 of 15			ENSP00000493607.1		A0A2R8Y3M9

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47374

AN:

151968

Hom.:

9095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0796

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.316

GnomAD2 exomes

AF:

0.374

AC:

94001

AN:

251360

AF XY:

0.380

show subpopulations

Gnomad AFR exome

AF:

0.0660

Gnomad AMR exome

AF:

0.389

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.228

Gnomad FIN exome

AF:

0.390

Gnomad NFE exome

AF:

0.429

Gnomad OTH exome

AF:

0.372

GnomAD4 exome

AF:

0.412

AC:

601509

AN:

1461168

Hom.:

127641

Cov.:

AF XY:

0.411

AC XY:

298976

AN XY:

726910

show subpopulations

Gnomad4 AFR exome

AF:

0.0628

AC:

2102

AN:

33470

Gnomad4 AMR exome

AF:

0.381

AC:

17047

AN:

44716

Gnomad4 ASJ exome

AF:

0.337

AC:

8812

AN:

26118

Gnomad4 EAS exome

AF:

0.228

AC:

9056

AN:

39682

Gnomad4 SAS exome

AF:

0.398

AC:

34347

AN:

86210

Gnomad4 FIN exome

AF:

0.394

AC:

21026

AN:

53414

Gnomad4 NFE exome

AF:

0.436

AC:

484680

AN:

1111428

Gnomad4 Remaining exome

AF:

0.377

AC:

22751

AN:

60364

Heterozygous variant carriers

17720

35440

53159

70879

88599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

14500

29000

43500

58000

72500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.312

AC:

47377

AN:

152088

Hom.:

9095

Cov.:

AF XY:

0.310

AC XY:

23062

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.0793

AC:

0.0793402

AN:

0.0793402

Gnomad4 AMR

AF:

0.356

AC:

0.355823

AN:

0.355823

Gnomad4 ASJ

AF:

0.341

AC:

0.340726

AN:

0.340726

Gnomad4 EAS

AF:

0.215

AC:

0.215254

AN:

0.215254

Gnomad4 SAS

AF:

0.385

AC:

0.384695

AN:

0.384695

Gnomad4 FIN

AF:

0.385

AC:

0.385235

AN:

0.385235

Gnomad4 NFE

AF:

0.431

AC:

0.43064

AN:

0.43064

Gnomad4 OTH

AF:

0.312

AC:

0.312027

AN:

0.312027

Heterozygous variant carriers

1510

3021

4531

6042

7552

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.376

Hom.:

33882

Bravo

AF:

0.296

Asia WGS

AF:

0.297

AC:

1034

AN:

3478

EpiCase

AF:

0.415

EpiControl

AF:

0.410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.20

CADD

Benign

9.7

DANN

Benign

0.65

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over