rs2413507

Variant names:

• chr22-38197421-A-G
• rs2413507
• ENST00000660610.1:c.-42+17032T>C

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000594306.1(PLA2G6):​c.-46+7872T>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 ENST00000594306.1 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G6	ENST00000660610.1	c.-42+17032T>C		intron_variant	Intron 1 of 16			ENSP00000499555.1
PLA2G6	ENST00000594306.1	c.-46+7872T>C		intron_variant	Intron 1 of 1	4		ENSP00000473160.1

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;