6-46720194-C-T

Variant names:

• chr6-46720194-C-T
• rs3799862
• NM_005084.4:c.109+2589G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005084.4(PLA2G7):​c.109+2589G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,122 control chromosomes in the GnomAD database, including 39,851 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 0.72 (39851 hom., cov: 33)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.109+2589G>A		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+2589G>A		intron_variant	Intron 2 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.109+2589G>A		intron_variant	Intron 2 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109680 AN: 152004 Hom.: 39829 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.721 AC: 109745 AN: 152122 Hom.: 39851 Cov.: 33 AF XY: 0.722 AC XY: 53682 AN XY: 74384

African (AFR) AF: 0.633 AC: 26273 AN: 41480

American (AMR) AF: 0.786 AC: 12008 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3990 AN: 5156

South Asian (SAS) AF: 0.752 AC: 3632 AN: 4830

European-Finnish (FIN) AF: 0.723 AC: 7667 AN: 10600

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51250 AN: 67982

Other (OTH) AF: 0.736 AC: 1555 AN: 2114

Alfa AF: 0.740 Hom.: 9519

Bravo AF: 0.718

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3799862; hg19: chr6-46687931;