chr6-46714342-A-C

Position:

• chr6-46714342-A-C

Variant summary

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

The NM_005084.4(PLA2G7):​c.470+118T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 776,726 control chromosomes in the GnomAD database, including 262,576 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 0.83 (52800 hom., cov: 30)
  • Exomes 𝑓: 0.82 (209776 hom.)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G7	NM_005084.4	c.470+118T>G		intron_variant		ENST00000274793.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G7	ENST00000274793.12	c.470+118T>G		intron_variant		1	NM_005084.4	P1
PLA2G7	ENST00000537365.1	c.470+118T>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126359 AN: 151900 Hom.: 52751 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.832

GnomAD4 exome AF: 0.818 AC: 511275 AN: 624710 Hom.: 209776 AF XY: 0.820 AC XY: 278916 AN XY: 340056

Gnomad4 AFR exome AF: 0.888

Gnomad4 AMR exome AF: 0.851

Gnomad4 ASJ exome AF: 0.823

Gnomad4 EAS exome AF: 0.887

Gnomad4 SAS exome AF: 0.874

Gnomad4 FIN exome AF: 0.746

Gnomad4 NFE exome AF: 0.802

Gnomad4 OTH exome AF: 0.816

GnomAD4 genome AF: 0.832 AC: 126466 AN: 152016 Hom.: 52800 Cov.: 30 AF XY: 0.832 AC XY: 61834 AN XY: 74292

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.832

Alfa AF: 0.803 Hom.: 54972

Bravo AF: 0.834

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.66

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: rs1362931; hg19: chr6-46682079;