dbSNP rs1362931: PLA2G7:c.470+118T>G (chr6-46714342-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005084.4(PLA2G7):c.470+118T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 776,726 control chromosomes in the GnomAD database, including 262,576 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 0.83 ( 52800 hom., cov: 30)

Exomes 𝑓: 0.82 ( 209776 hom. )

Consequence

PLA2G7
NM_005084.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

17 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:

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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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005084.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G7	NM_005084.4	MANE Select	c.470+118T>G		intron	N/A	NP_005075.3
	PLA2G7	NM_001168357.2		c.470+118T>G		intron	N/A	NP_001161829.1	Q13093

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PLA2G7	ENST00000274793.12	TSL:1 MANE Select	c.470+118T>G	intron	N/A	ENSP00000274793.7	Q13093
PLA2G7	ENST00000537365.1	TSL:1	c.470+118T>G	intron	N/A	ENSP00000445666.1	Q13093
PLA2G7	ENST00000878321.1		c.470+118T>G	intron	N/A	ENSP00000548380.1

Frequencies

GnomAD3 genomes

AF:

0.832

AC:

126359

AN:

151900

Hom.:

52751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.616

Gnomad AMR

AF:

0.846

Gnomad ASJ

AF:

0.819

Gnomad EAS

AF:

0.885

Gnomad SAS

AF:

0.888

Gnomad FIN

AF:

0.754

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.801

Gnomad OTH

AF:

0.832

GnomAD4 exome

AF:

0.818

AC:

511275

AN:

624710

Hom.:

209776

AF XY:

0.820

AC XY:

278916

AN XY:

340056

show subpopulations

African (AFR)

AF:

0.888

AC:

15673

AN:

17640

American (AMR)

AF:

0.851

AC:

36050

AN:

42362

Ashkenazi Jewish (ASJ)

AF:

0.823

AC:

17183

AN:

20890

East Asian (EAS)

AF:

0.887

AC:

31633

AN:

35668

South Asian (SAS)

AF:

0.874

AC:

59851

AN:

68444

European-Finnish (FIN)

AF:

0.746

AC:

32936

AN:

44126

Middle Eastern (MID)

AF:

0.864

AC:

3582

AN:

4144

European-Non Finnish (NFE)

AF:

0.802

AC:

287387

AN:

358372

Other (OTH)

AF:

0.816

AC:

26980

AN:

33064

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5287

10574

15861

21148

26435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1660

3320

4980

6640

8300

<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:

0.832

AC:

126466

AN:

152016

Hom.:

52800

Cov.:

AF XY:

0.832

AC XY:

61834

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.889

AC:

36876

AN:

41474

American (AMR)

AF:

0.847

AC:

12919

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.819

AC:

2842

AN:

3470

East Asian (EAS)

AF:

0.885

AC:

4565

AN:

5160

South Asian (SAS)

AF:

0.888

AC:

4282

AN:

4820

European-Finnish (FIN)

AF:

0.754

AC:

7967

AN:

10562

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.801

AC:

54464

AN:

67964

Other (OTH)

AF:

0.832

AC:

1750

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1036

2072

3107

4143

5179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.811

Hom.:

138389

Bravo

AF:

0.834

Asia WGS

AF:

0.891

AC:

3099

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.61

(source)

DANN

Benign

0.66

PhyloP100

-0.37

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over