22-38167464-C-T

Variant summary

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

The NM_003560.4(PLA2G6):c.209+1754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,772 control chromosomes in the GnomAD database, including 20,224 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 0.51 (20224 hom., cov: 31)
• Consequence: PLA2G6 NM_003560.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

PLA2G6 (HGNC:9039): (phospholipase A2 group VI) The protein encoded by this gene is an A2 phospholipase, a class of enzyme that catalyzes the release of fatty acids from phospholipids. The encoded protein may play a role in phospholipid remodelling, arachidonic acid release, leukotriene and prostaglandin synthesis, fas-mediated apoptosis, and transmembrane ion flux in glucose-stimulated B-cells. Several transcript variants encoding multiple isoforms have been described, but the full-length nature of only three of them have been determined to date. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G6	NM_003560.4	c.209+1754G>A		intron_variant		ENST00000332509.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G6	ENST00000332509.8	c.209+1754G>A		intron_variant		1	NM_003560.4	P3

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77107 AN: 151654 Hom.: 20193 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.509 AC: 77204 AN: 151772 Hom.: 20224 Cov.: 31 AF XY: 0.509 AC XY: 37728 AN XY: 74168

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.493

Alfa AF: 0.478 Hom.: 36088

Bravo AF: 0.516

Asia WGS AF: 0.551 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.0
Dann	Benign	0.68

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: rs132985; hg19: chr22-38563471;