6-46719682-C-T

Variant names:

• chr6-46719682-C-T
• rs12195701
• NM_005084.4:c.110-2586G>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.110-2586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,136 control chromosomes in the GnomAD database, including 2,272 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 0.15 (2272 hom., cov: 33)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.110-2586G>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.110-2586G>A		intron_variant	Intron 2 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.110-2586G>A		intron_variant	Intron 2 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23486 AN: 152018 Hom.: 2270 Cov.: 33

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.154 AC: 23487 AN: 152136 Hom.: 2272 Cov.: 33 AF XY: 0.156 AC XY: 11584 AN XY: 74372

African (AFR) AF: 0.0459 AC: 1904 AN: 41508

American (AMR) AF: 0.130 AC: 1988 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.132 AC: 683 AN: 5170

South Asian (SAS) AF: 0.271 AC: 1303 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2249 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13784 AN: 67980

Other (OTH) AF: 0.169 AC: 357 AN: 2112

Alfa AF: 0.201 Hom.: 2657

Bravo AF: 0.139

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		0.33
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: rs12195701; hg19: chr6-46687419;