Genetic Variant PLA2G6:c.-42+15220G>A (chr22-38199233-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.782

Variant links:

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]

PLA2G6 links:

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ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G6	ENST00000660610.1 link	c.-42+15220G>A		intron_variant	Intron 1 of 16			ENSP00000499555.1		O60733-1
PLA2G6	ENST00000594306.1 link	c.-46+6060G>A		intron_variant	Intron 1 of 1	4		ENSP00000473160.1		M0R3D9

Frequencies

GnomAD3 genomes

AF:

0.525

AC:

79558

AN:

151520

Hom.:

21820

Cov.:

show subpopulations

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.:

AF XY:

0.523

AC XY:

38758

AN XY:

74068

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over