Genetic Variant PLA2G15:c.-51A>T (chr16-68245376-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012320.4(PLA2G15):c.-51A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00934 in 1,582,552 control chromosomes in the GnomAD database, including 753 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 0.040 ( 378 hom., cov: 32)

Exomes 𝑓: 0.0061 ( 375 hom. )

Consequence

PLA2G15
NM_012320.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.228

Publications

1 publications found

Variant links:

Genes affected

PLA2G15 (HGNC:17163): (phospholipase A2 group XV) Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. The protein encoded by this gene hydrolyzes lysophosphatidylcholine to glycerophosphorylcholine and a free fatty acid. This enzyme is present in the plasma and thought to be associated with high-density lipoprotein. A later paper contradicts the function of this gene. It demonstrates that this gene encodes a lysosomal enzyme instead of a lysophospholipase and has both calcium-independent phospholipase A2 and transacylase activities. [provided by RefSeq, Jul 2008]

PLA2G15 links:

ENSG00000307195 (HGNC:):

ENSG00000307195 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
PLA2G15	NM_012320.4 link	c.-51A>T	5_prime_UTR_variant	Exon 1 of 6	ENST00000219345.10	NP_036452.1
PLA2G15	NM_001363551.2 link	c.-51A>T	5_prime_UTR_variant	Exon 1 of 6		NP_001350480.1
PLA2G15	XM_011522979.3 link	c.-51A>T	5_prime_UTR_variant	Exon 1 of 7		XP_011521281.1
PLA2G15	XM_011522980.4 link	c.-51A>T	5_prime_UTR_variant	Exon 1 of 7		XP_011521282.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G15	ENST00000219345.10 link	c.-51A>T		5_prime_UTR_variant	Exon 1 of 6	1	NM_012320.4	ENSP00000219345.5

Frequencies

GnomAD3 genomes

AF:

0.0401

AC:

6105

AN:

152110

Hom.:

374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0183

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00231

Gnomad OTH

AF:

0.0307

GnomAD2 exomes

AF:

0.0117

AC:

2674

AN:

228658

AF XY:

0.00908

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.00893

Gnomad ASJ exome

AF:

0.00873

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00252

Gnomad NFE exome

AF:

0.00215

Gnomad OTH exome

AF:

0.00667

GnomAD4 exome

AF:

0.00605

AC:

8659

AN:

1430324

Hom.:

375

Cov.:

AF XY:

0.00550

AC XY:

3905

AN XY:

710020

show subpopulations

African (AFR)

AF:

0.144

AC:

4736

AN:

32776

American (AMR)

AF:

0.0100

AC:

431

AN:

43062

Ashkenazi Jewish (ASJ)

AF:

0.0106

AC:

269

AN:

25394

East Asian (EAS)

AF:

0.0000256

AC:

AN:

39036

South Asian (SAS)

AF:

0.000469

AC:

AN:

85364

European-Finnish (FIN)

AF:

0.00252

AC:

AN:

39284

Middle Eastern (MID)

AF:

0.0234

AC:

133

AN:

5688

European-Non Finnish (NFE)

AF:

0.00201

AC:

2209

AN:

1100402

Other (OTH)

AF:

0.0125

AC:

741

AN:

59318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

363

725

1088

1450

1813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<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:

0.0402

AC:

6124

AN:

152228

Hom.:

378

Cov.:

AF XY:

0.0387

AC XY:

2883

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.134

AC:

5557

AN:

41514

American (AMR)

AF:

0.0183

AC:

280

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0118

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.000622

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00132

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00231

AC:

157

AN:

68012

Other (OTH)

AF:

0.0299

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

288

577

865

1154

1442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.0236

Hom.:

Bravo

AF:

0.0449

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

9.6

(source)

DANN

Benign

0.63

PhyloP100

-0.23

PromoterAI

-0.025

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over