rs3891103

Positions:

• chr22-38141152-C-G

Variant summary

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

The NM_003560.4(PLA2G6):​c.610-983G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,404 control chromosomes in the GnomAD database, including 14,218 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 0.43 (14217 hom., cov: 28)
  • Exomes 𝑓: 0.23 (1 hom.)
• Consequence: PLA2G6 NM_003560.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

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]

(HGNC:):

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 = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G6	NM_003560.4	c.610-983G>C		intron_variant		ENST00000332509.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G6	ENST00000332509.8	c.610-983G>C		intron_variant		1	NM_003560.4	P3
	ENST00000624072.1	n.10937C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 64943 AN: 151224 Hom.: 14214 Cov.: 28

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.440

GnomAD4 exome AF: 0.226 AC: 14 AN: 62 Hom.: 1 Cov.: 0 AF XY: 0.239 AC XY: 11 AN XY: 46

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.429 AC: 64991 AN: 151342 Hom.: 14217 Cov.: 28 AF XY: 0.430 AC XY: 31789 AN XY: 73926

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.443

Alfa AF: 0.417 Hom.: 1636

Bravo AF: 0.432

Asia WGS AF: 0.466 AC: 1623 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.29

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: rs3891103; hg19: chr22-38537159;