rs5750558

Positions:

• chr22-38186490-G-A
• chr22-38186490-G-C
• chr22-38186490-G-T

Variant summary

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

The ENST00000660610.1(PLA2G6):​c.-41-17023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,698 control chromosomes in the GnomAD database, including 19,958 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 0.50 (19958 hom., cov: 30)
• Consequence: PLA2G6 ENST00000660610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

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=-0.78).
• 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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G6	ENST00000594306.1	c.-45-17019C>T		intron_variant		4
PLA2G6	ENST00000660610.1	c.-41-17023C>T		intron_variant				P3
PLA2G6	ENST00000417303.6	n.68+5543C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76358 AN: 151580 Hom.: 19967 Cov.: 30

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.503 AC: 76364 AN: 151698 Hom.: 19958 Cov.: 30 AF XY: 0.502 AC XY: 37168 AN XY: 74104

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.523

Alfa AF: 0.534 Hom.: 2769

Bravo AF: 0.496

Asia WGS AF: 0.457 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5750558; hg19: chr22-38582497;