Genetic Variant PLA2G7:c.-261T>C (chr6-46735776-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001168357.2(PLA2G7):c.-261T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,160 control chromosomes in the GnomAD database, including 22,448 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 0.51 ( 22445 hom., cov: 33)

Exomes 𝑓: 0.26 ( 3 hom. )

Consequence

PLA2G7
NM_001168357.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Publications

29 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
PLA2G7	NM_001168357.2 link	c.-261T>C	upstream_gene_variant	NP_001161829.1	Q13093
PLA2G7	XM_005249408.5 link	c.-193T>C	upstream_gene_variant	XP_005249465.1	Q13093
PLA2G7	XM_047419359.1 link	c.-185T>C	upstream_gene_variant	XP_047275315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000537365.1 link	c.-261T>C		upstream_gene_variant		1		ENSP00000445666.1		Q13093

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77804

AN:

152000

Hom.:

22398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.664

Gnomad FIN

AF:

0.352

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.511

GnomAD4 exome

AF:

0.262

AC:

AN:

Hom.:

AF XY:

0.281

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.405

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.512

AC:

77909

AN:

152118

Hom.:

22445

Cov.:

AF XY:

0.511

AC XY:

37996

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.777

AC:

32228

AN:

41496

American (AMR)

AF:

0.513

AC:

7839

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.526

AC:

1823

AN:

3468

East Asian (EAS)

AF:

0.269

AC:

1389

AN:

5160

South Asian (SAS)

AF:

0.663

AC:

3201

AN:

4828

European-Finnish (FIN)

AF:

0.352

AC:

3722

AN:

10582

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.385

AC:

26153

AN:

67986

Other (OTH)

AF:

0.512

AC:

1079

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1754

3509

5263

7018

8772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.433

Hom.:

44194

Bravo

AF:

0.528

Asia WGS

AF:

0.529

AC:

1843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.1

(source)

DANN

Benign

0.39

PhyloP100

-1.5

PromoterAI

-0.0048

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

chr6-46735776-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over