rs3761445

Variant names:

• chr22-38199404-G-A
• rs3761445
• ENST00000660610.1:c.-42+15049C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-38199404-G-A
• chr22-38199404-G-C

Variant summary

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

The ENST00000594306.1(PLA2G6):​c.-46+5889C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,858 control chromosomes in the GnomAD database, including 21,961 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 0.53 (21961 hom., cov: 30)
• Consequence: PLA2G6 ENST00000594306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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+15049C>T		intron_variant	Intron 1 of 16			ENSP00000499555.1
PLA2G6	ENST00000594306.1	c.-46+5889C>T		intron_variant	Intron 1 of 1	4		ENSP00000473160.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79825 AN: 151740 Hom.: 21978 Cov.: 30

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.526 AC: 79838 AN: 151858 Hom.: 21961 Cov.: 30 AF XY: 0.525 AC XY: 38919 AN XY: 74176

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.540

Alfa AF: 0.577 Hom.: 16565

Bravo AF: 0.518

Asia WGS AF: 0.553 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
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: rs3761445; hg19: chr22-38595411;