22-38199233-C-T

Position:

• chr22-38199233-C-T

Variant summary

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

The ENST00000594306.1(PLA2G6):​c.-46+6060G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,640 control chromosomes in the GnomAD database, including 21,804 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 0.52 (21804 hom., cov: 32)
• Consequence: PLA2G6 ENST00000594306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38199233C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G6	ENST00000660610.1	c.-42+15220G>A		intron_variant				ENSP00000499555.1
PLA2G6	ENST00000594306.1	c.-46+6060G>A		intron_variant		4		ENSP00000473160.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79558 AN: 151520 Hom.: 21820 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.525 AC: 79573 AN: 151640 Hom.: 21804 Cov.: 32 AF XY: 0.523 AC XY: 38758 AN XY: 74068

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.540

Alfa AF: 0.536 Hom.: 4197

Bravo AF: 0.518

Asia WGS AF: 0.553 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756968; hg19: chr22-38595240; COSMIC: COSV58299342;