6-46722025-T-C

Variant names:

• chr6-46722025-T-C
• rs9472830
• NM_005084.4:c.109+758A>G

Variant summary

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

The NM_005084.4(PLA2G7):​c.109+758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,034 control chromosomes in the GnomAD database, including 52,808 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 (52808 hom., cov: 30)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

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 rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.109+758A>G		intron_variant	Intron 2 of 11	ENST00000274793.12	NP_005075.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12	c.109+758A>G		intron_variant	Intron 2 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.109+758A>G		intron_variant	Intron 2 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126378 AN: 151914 Hom.: 52759 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.832 AC: 126485 AN: 152034 Hom.: 52808 Cov.: 30 AF XY: 0.832 AC XY: 61831 AN XY: 74306

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.831

Alfa AF: 0.811 Hom.: 30196

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	0.38
DANN	Benign	0.45

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: rs9472830; hg19: chr6-46689762;