dbSNP rs9395208: PLA2G7:c.-67C>G (chr6-46735582-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000537365.1(PLA2G7):c.-67C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,576 control chromosomes in the GnomAD database, including 3,556 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 0.21 ( 3548 hom., cov: 33)

Exomes 𝑓: 0.20 ( 8 hom. )

Consequence

PLA2G7
ENST00000537365.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.45

Publications

8 publications found

Variant links:

Genes affected

PLA2G7 (HGNC:9040): (phospholipase A2 group VII) The protein encoded by this gene is a secreted enzyme that catalyzes the degradation of platelet-activating factor to biologically inactive products. Defects in this gene are a cause of platelet-activating factor acetylhydrolase deficiency. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2009]

PLA2G7 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4 link	c.-437C>G		upstream_gene_variant		ENST00000274793.12	NP_005075.3	Q13093

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PLA2G7	ENST00000537365.1 link	c.-67C>G	5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 12	1		ENSP00000445666.1	Q13093
PLA2G7	ENST00000537365.1 link	c.-67C>G	5_prime_UTR_variant	Exon 1 of 12	1		ENSP00000445666.1	Q13093
PLA2G7	ENST00000274793.12 link	c.-437C>G	upstream_gene_variant		1	NM_005084.4	ENSP00000274793.7	Q13093

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31231

AN:

152164

Hom.:

3540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.204

AC:

AN:

294

Hom.:

Cov.:

AF XY:

0.212

AC XY:

AN XY:

208

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.375

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.198

AC:

AN:

242

Other (OTH)

AF:

0.200

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.205

AC:

31262

AN:

152282

Hom.:

3548

Cov.:

AF XY:

0.212

AC XY:

15814

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.142

AC:

5894

AN:

41574

American (AMR)

AF:

0.289

AC:

4430

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

981

AN:

3470

East Asian (EAS)

AF:

0.164

AC:

848

AN:

5174

South Asian (SAS)

AF:

0.458

AC:

2209

AN:

4826

European-Finnish (FIN)

AF:

0.228

AC:

2413

AN:

10600

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13767

AN:

68014

Other (OTH)

AF:

0.221

AC:

467

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1295

2591

3886

5182

6477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.208

Hom.:

427

Bravo

AF:

0.198

Asia WGS

AF:

0.329

AC:

1141

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.063

(source)

DANN

Benign

0.49

PhyloP100

-2.4

PromoterAI

-0.018

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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