rs9395208

Variant names:

• chr6-46735582-G-C
• rs9395208
• ENST00000537365.1:c.-67C>G

Variant summary

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

The NM_001168357.2(PLA2G7):​c.-67C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,576 control chromosomes in the GnomAD database, including 3,556 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 0.21 (3548 hom., cov: 33)
  • Exomes 𝑓: 0.20 (8 hom.)
• Consequence: PLA2G7 NM_001168357.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.-437C>G		upstream_gene_variant		ENST00000274793.12	NP_005075.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000537365.1	c.-67C>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 12	1		ENSP00000445666.1
PLA2G7	ENST00000537365.1	c.-67C>G		5_prime_UTR_variant	Exon 1 of 12	1		ENSP00000445666.1
PLA2G7	ENST00000274793.12	c.-437C>G		upstream_gene_variant		1	NM_005084.4	ENSP00000274793.7

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31231 AN: 152164 Hom.: 3540 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.218

GnomAD4 exome AF: 0.204 AC: 60 AN: 294 Hom.: 8 Cov.: 0 AF XY: 0.212 AC XY: 44 AN XY: 208

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.198

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.205 AC: 31262 AN: 152282 Hom.: 3548 Cov.: 33 AF XY: 0.212 AC XY: 15814 AN XY: 74444

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.221

Alfa AF: 0.208 Hom.: 427

Bravo AF: 0.198

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.063
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9395208; hg19: chr6-46703319;