rs2413507

Positions:

• chr22-38197421-A-G
• chr22-38197421-A-T

Variant summary

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

The ENST00000660610.1(PLA2G6):​c.-42+17032T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,636 control chromosomes in the GnomAD database, including 20,408 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 (20408 hom., cov: 30)
• Consequence: PLA2G6 ENST00000660610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

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=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G6	ENST00000594306.1	c.-46+7872T>C		intron_variant		4		ENSP00000473160
PLA2G6	ENST00000660610.1	c.-42+17032T>C		intron_variant				ENSP00000499555	P3

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77489 AN: 151522 Hom.: 20407 Cov.: 30

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.511 AC: 77526 AN: 151636 Hom.: 20408 Cov.: 30 AF XY: 0.511 AC XY: 37843 AN XY: 74086

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.511

Alfa AF: 0.529 Hom.: 2621

Bravo AF: 0.503

Asia WGS AF: 0.466 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.4
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2413507; hg19: chr22-38593428;