ENST00000660610.1:c.-42+15200T>A

Variant names:

• chr22-38199253-A-T
• rs5750561
• ENST00000660610.1:c.-42+15200T>A

Variant summary

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

The ENST00000660610.1(PLA2G6):​c.-42+15200T>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 151,672 control chromosomes in the GnomAD database, including 21,827 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 (21827 hom., cov: 32)
• Consequence: PLA2G6 ENST00000660610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G6	ENST00000660610.1	c.-42+15200T>A		intron_variant	Intron 1 of 16			ENSP00000499555.1
PLA2G6	ENST00000594306.1	c.-46+6040T>A		intron_variant	Intron 1 of 1	4		ENSP00000473160.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79609 AN: 151556 Hom.: 21845 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: 0.738

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.484

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: 79620 AN: 151672 Hom.: 21827 Cov.: 32 AF XY: 0.524 AC XY: 38789 AN XY: 74082

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: 0.609

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.540

Alfa AF: 0.557 Hom.: 3019

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	-0.87
CADD	Benign	7.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5750561; hg19: chr22-38595260;