6-46717549-T-C

Position:

• chr6-46717549-T-C

Variant summary

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

The NM_005084.4(PLA2G7):​c.110-453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,722 control chromosomes in the GnomAD database, including 39,055 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 0.71 (39055 hom., cov: 28)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G7	NM_005084.4	c.110-453A>G		intron_variant		ENST00000274793.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G7	ENST00000274793.12	c.110-453A>G		intron_variant		1	NM_005084.4	P1
PLA2G7	ENST00000537365.1	c.110-453A>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108300 AN: 151604 Hom.: 39034 Cov.: 28

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.714 AC: 108363 AN: 151722 Hom.: 39055 Cov.: 28 AF XY: 0.714 AC XY: 52943 AN XY: 74136

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.731

Alfa AF: 0.745 Hom.: 86827

Bravo AF: 0.710

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.41

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: rs6929105; hg19: chr6-46685286;