rs7756935

Variant names:

• chr6-46707288-C-A
• rs7756935
• NM_005084.4:c.1040+703G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-46707288-C-A
• chr6-46707288-C-G

Variant summary

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

The NM_005084.4(PLA2G7):​c.1040+703G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,052 control chromosomes in the GnomAD database, including 47,623 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 0.79 (47623 hom., cov: 31)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 32 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.1040+703G>T		intron_variant	Intron 10 of 11	ENST00000274793.12	NP_005075.3
PLA2G7	NM_001168357.2	c.1040+703G>T		intron_variant	Intron 10 of 11		NP_001161829.1
PLA2G7	XM_005249408.5	c.1040+703G>T		intron_variant	Intron 10 of 11		XP_005249465.1
PLA2G7	XM_047419359.1	c.905+703G>T		intron_variant	Intron 9 of 10		XP_047275315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12	c.1040+703G>T		intron_variant	Intron 10 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.1040+703G>T		intron_variant	Intron 10 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120135 AN: 151934 Hom.: 47598 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.791 AC: 120213 AN: 152052 Hom.: 47623 Cov.: 31 AF XY: 0.791 AC XY: 58744 AN XY: 74298

African (AFR) AF: 0.754 AC: 31251 AN: 41448

American (AMR) AF: 0.823 AC: 12566 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4575 AN: 5170

South Asian (SAS) AF: 0.855 AC: 4121 AN: 4818

European-Finnish (FIN) AF: 0.760 AC: 8035 AN: 10570

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54436 AN: 67992

Other (OTH) AF: 0.798 AC: 1682 AN: 2108

Alfa AF: 0.794 Hom.: 60885

Bravo AF: 0.787

Asia WGS AF: 0.862 AC: 2996 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	0.48
DANN	Benign	0.42
PhyloP100		-0.51
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: rs7756935; hg19: chr6-46675025;