Variant chr6-46704715-TAATC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_005084.4(PLA2G7):c.1190-23_1190-20delGATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,467,096 control chromosomes in the GnomAD database, including 102,008 homozygotes. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.30 ( 8581 hom., cov: 17)

Exomes 𝑓: 0.37 ( 93427 hom. )

Consequence

PLA2G7
NM_005084.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.72

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 6-46704715-TAATC-T is Benign according to our data. Variant chr6-46704715-TAATC-T is described in ClinVar as [Benign]. Clinvar id is 1252749.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PLA2G7	NM_005084.4 linkuse as main transcript	c.1190-23_1190-20delGATT	intron_variant	ENST00000274793.12	NP_005075.3	Q13093
PLA2G7	NM_001168357.2 linkuse as main transcript	c.1190-23_1190-20delGATT	intron_variant		NP_001161829.1	Q13093
PLA2G7	XM_005249408.5 linkuse as main transcript	c.1190-23_1190-20delGATT	intron_variant		XP_005249465.1	Q13093
PLA2G7	XM_047419359.1 linkuse as main transcript	c.1055-23_1055-20delGATT	intron_variant		XP_047275315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12 linkuse as main transcript	c.1190-23_1190-20delGATT		intron_variant		1	NM_005084.4	ENSP00000274793.7		Q13093
PLA2G7	ENST00000537365.1 linkuse as main transcript	c.1190-23_1190-20delGATT		intron_variant		1		ENSP00000445666.1		Q13093

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45603

AN:

151630

Hom.:

8577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.559

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.295

GnomAD3 exomes

AF:

0.351

AC:

86828

AN:

247356

Hom.:

16703

AF XY:

0.347

AC XY:

46469

AN XY:

133818

show subpopulations

Gnomad AFR exome

AF:

0.0673

Gnomad AMR exome

AF:

0.359

Gnomad ASJ exome

AF:

0.300

Gnomad EAS exome

AF:

0.573

Gnomad SAS exome

AF:

0.196

Gnomad FIN exome

AF:

0.391

Gnomad NFE exome

AF:

0.393

Gnomad OTH exome

AF:

0.335

GnomAD4 exome

AF:

0.367

AC:

482785

AN:

1315348

Hom.:

93427

AF XY:

0.364

AC XY:

240880

AN XY:

662240

show subpopulations

Gnomad4 AFR exome

AF:

0.0613

Gnomad4 AMR exome

AF:

0.354

Gnomad4 ASJ exome

AF:

0.304

Gnomad4 EAS exome

AF:

0.512

Gnomad4 SAS exome

AF:

0.198

Gnomad4 FIN exome

AF:

0.393

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.301

AC:

45615

AN:

151748

Hom.:

8581

Cov.:

AF XY:

0.301

AC XY:

22303

AN XY:

74114

show subpopulations

Gnomad4 AFR

AF:

0.0769

Gnomad4 AMR

AF:

0.326

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.385

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.351

Hom.:

1900

Bravo

AF:

0.290

Asia WGS

AF:

0.327

AC:

1133

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 19, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BranchPoint Hunter

5.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over