rs2216465

Positions:

• chr6-46708282-C-G

Variant summary

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

The NM_005084.4(PLA2G7):​c.870-121G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 780,950 control chromosomes in the GnomAD database, including 57,228 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 0.38 (11155 hom., cov: 32)
  • Exomes 𝑓: 0.37 (46073 hom.)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.870-121G>C		intron_variant		ENST00000274793.12	NP_005075.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12	c.870-121G>C		intron_variant		1	NM_005084.4	ENSP00000274793	P1
PLA2G7	ENST00000537365.1	c.870-121G>C		intron_variant		1		ENSP00000445666	P1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57364 AN: 151792 Hom.: 11157 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.383

GnomAD4 exome AF: 0.371 AC: 233070 AN: 629040 Hom.: 46073 AF XY: 0.381 AC XY: 129155 AN XY: 338800

Gnomad4 AFR exome AF: 0.443

Gnomad4 AMR exome AF: 0.417

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.377

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.313

Gnomad4 NFE exome AF: 0.326

Gnomad4 OTH exome AF: 0.359

GnomAD4 genome AF: 0.378 AC: 57406 AN: 151910 Hom.: 11155 Cov.: 32 AF XY: 0.381 AC XY: 28270 AN XY: 74270

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.387

Alfa AF: 0.352 Hom.: 1310

Bravo AF: 0.376

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2216465; hg19: chr6-46676019;