rs2899297

chr22-38198661-G-A

Variant summary

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

The ENST00000660610.1(PLA2G6):c.-42+15792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,878 control chromosomes in the GnomAD database, including 22,060 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 0.53 (22060 hom., cov: 31)
• Consequence: PLA2G6 ENST00000660610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G6	ENST00000594306.1	c.-46+6632C>T		intron_variant		4
PLA2G6	ENST00000660610.1	c.-42+15792C>T		intron_variant				P3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80066 AN: 151760 Hom.: 22074 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.527 AC: 80084 AN: 151878 Hom.: 22060 Cov.: 31 AF XY: 0.526 AC XY: 39069 AN XY: 74214

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.541

Alfa AF: 0.565 Hom.: 8418

Bravo AF: 0.519

Asia WGS AF: 0.553 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.53
Dann	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2899297; hg19: chr22-38594668;