dbSNP rs2216465: PLA2G7:c.870-121G>C (chr6-46708282-C-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_005084.4(PLA2G7):c.870-121G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 780,950 control chromosomes in the GnomAD database, including 57,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.38 ( 11155 hom., cov: 32)

Exomes 𝑓: 0.37 ( 46073 hom. )

Consequence

PLA2G7
NM_005084.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Publications

13 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.602 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.870-121G>C		intron	N/A	NP_005075.3
	PLA2G7	NM_001168357.2		c.870-121G>C		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.870-121G>C	intron	N/A	ENSP00000274793.7	Q13093
PLA2G7	ENST00000537365.1	TSL:1	c.870-121G>C	intron	N/A	ENSP00000445666.1	Q13093
PLA2G7	ENST00000878321.1		c.870-121G>C	intron	N/A	ENSP00000548380.1

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57364

AN:

151792

Hom.:

11157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.446

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.383

GnomAD4 exome

AF:

0.371

AC:

233070

AN:

629040

Hom.:

46073

AF XY:

0.381

AC XY:

129155

AN XY:

338800

show subpopulations

African (AFR)

AF:

0.443

AC:

7925

AN:

17896

American (AMR)

AF:

0.417

AC:

16284

AN:

39084

Ashkenazi Jewish (ASJ)

AF:

0.400

AC:

8171

AN:

20452

East Asian (EAS)

AF:

0.377

AC:

13240

AN:

35146

South Asian (SAS)

AF:

0.600

AC:

40049

AN:

66712

European-Finnish (FIN)

AF:

0.313

AC:

13934

AN:

44462

Middle Eastern (MID)

AF:

0.430

AC:

1670

AN:

3886

European-Non Finnish (NFE)

AF:

0.326

AC:

119929

AN:

368326

Other (OTH)

AF:

0.359

AC:

11868

AN:

33076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

7180

14361

21541

28722

35902

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1306

2612

3918

5224

6530

<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:

0.378

AC:

57406

AN:

151910

Hom.:

11155

Cov.:

AF XY:

0.381

AC XY:

28270

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.446

AC:

18469

AN:

41414

American (AMR)

AF:

0.402

AC:

6141

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.387

AC:

1341

AN:

3466

East Asian (EAS)

AF:

0.321

AC:

1658

AN:

5158

South Asian (SAS)

AF:

0.621

AC:

2984

AN:

4806

European-Finnish (FIN)

AF:

0.330

AC:

3475

AN:

10546

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.326

AC:

22140

AN:

67936

Other (OTH)

AF:

0.387

AC:

818

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1823

3646

5468

7291

9114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.352

Hom.:

1310

Bravo

AF:

0.376

Asia WGS

AF:

0.504

AC:

1753

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.28

(source)

DANN

Benign

0.34

PhyloP100

-1.7

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over