rs3799863

chr6-46720054-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005084.4(PLA2G7):c.109+2729T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,198 control chromosomes in the GnomAD database, including 311 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 0.058 (311 hom., cov: 33)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G7	NM_005084.4	c.109+2729T>A		intron_variant		ENST00000274793.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G7	ENST00000274793.12	c.109+2729T>A		intron_variant		1	NM_005084.4	P1
PLA2G7	ENST00000537365.1	c.109+2729T>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0578 AC: 8783 AN: 152080 Hom.: 311 Cov.: 33

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0578 AC: 8791 AN: 152198 Hom.: 311 Cov.: 33 AF XY: 0.0575 AC XY: 4282 AN XY: 74406

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.0349

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0499 Hom.: 24

Bravo AF: 0.0576

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.54

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: rs3799863; hg19: chr6-46687791;