6-46704715-TAATC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005084.4(PLA2G7):c.1190-23_1190-20del 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 (★).

• Frequency:
  • Genomes: 𝑓 0.30 (8581 hom., cov: 17)
  • Exomes 𝑓: 0.37 (93427 hom.)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.72

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]

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G7	NM_005084.4	c.1190-23_1190-20del		intron_variant		ENST00000274793.12
PLA2G7	NM_001168357.2	c.1190-23_1190-20del		intron_variant
PLA2G7	XM_005249408.5	c.1190-23_1190-20del		intron_variant
PLA2G7	XM_047419359.1	c.1055-23_1055-20del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G7	ENST00000274793.12	c.1190-23_1190-20del		intron_variant		1	NM_005084.4	P1
PLA2G7	ENST00000537365.1	c.1190-23_1190-20del		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45603 AN: 151630 Hom.: 8577 Cov.: 17

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

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

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.: 17 AF XY: 0.301 AC XY: 22303 AN XY: 74114

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

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
La Branchor		0.38

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

Other links and lift over

dbSNP: rs148052037; hg19: chr6-46672452;