Variant 22-38201371-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000594306.1(PLA2G6):c.-46+3922C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,788 control chromosomes in the GnomAD database, including 20,436 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 ( 20425 hom., cov: 31)

Exomes 𝑓: 0.45 ( 11 hom. )

Consequence

PLA2G6
ENST00000594306.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.136

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:

MAFF (HGNC:6780): (MAF bZIP transcription factor F) The protein encoded by this gene is a basic leucine zipper (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. The encoded protein can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. This gene may also be involved in the cellular stress response. Multiple transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]

MAFF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
PLA2G6	ENST00000660610.1 link	c.-42+13082C>A	intron_variant	Intron 1 of 16		ENSP00000499555.1	O60733-1
PLA2G6	ENST00000594306.1 link	c.-46+3922C>A	intron_variant	Intron 1 of 1	4	ENSP00000473160.1	M0R3D9
MAFF	ENST00000624676.1 link	n.605G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78125

AN:

151566

Hom.:

20427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.379

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.558

Gnomad OTH

AF:

0.528

GnomAD4 exome

AF:

0.452

AC:

AN:

104

Hom.:

Cov.:

AF XY:

0.423

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.625

Gnomad4 NFE exome

AF:

0.457

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.515

AC:

78161

AN:

151684

Hom.:

20425

Cov.:

AF XY:

0.512

AC XY:

37974

AN XY:

74100

show subpopulations

Gnomad4 AFR

AF:

0.449

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.546

Gnomad4 EAS

AF:

0.501

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.588

Gnomad4 NFE

AF:

0.558

Gnomad4 OTH

AF:

0.524

Alfa

AF:

0.545

Hom.:

8507

Bravo

AF:

0.511

Asia WGS

AF:

0.427

AC:

1482

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

4.4

DANN

Benign

0.73

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