Variant 15-41842325-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001114633.2(PLA2G4B):c.705+49C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 1,608,608 control chromosomes in the GnomAD database, including 512,612 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 0.76 ( 44409 hom., cov: 32)

Exomes 𝑓: 0.80 ( 468203 hom. )

Consequence

PLA2G4B
NM_001114633.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.322

Variant links:

Genes affected

PLA2G4B (HGNC:9036): (phospholipase A2 group IVB) This gene encodes a member of the cytosolic phospholipase A2 protein family. Phospholipase A2 enzymes hydrolyze the sn-2 bond of phospholipids, releasing lysophospholipids and fatty acids. This enzyme may be associated with mitochondria and early endosomes. Most tissues also express read-through transcripts from the upstream gene into this gene, some of which may encode fusion proteins combining the N-terminus of the upstream gene including its JmjC domain with the almost complete coding region of this gene, including the C2 and cytoplasmic phospholipase A2 domains. [provided by RefSeq, Jul 2008]

PLA2G4B links:

JMJD7-PLA2G4B (HGNC:34449): (JMJD7-PLA2G4B readthrough) This locus represents naturally-occurring readthrough transcription between the neighboring jumonji domain containing 7 (JMJD7) and phospholipase A2, group IVB (cytosolic) (PLA2G4B) genes. Readthrough transcripts encode fusion proteins that share amino acid sequence with each individual gene product, including a partial JmjC domain and downstream C2 and phospholipase A2 domains. Alternatively spliced transcript variants have been observed. [provided by RefSeq, Oct 2013]

JMJD7-PLA2G4B 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PLA2G4B	NM_001114633.2 link	c.705+49C>T	intron_variant	ENST00000458483.4	NP_001108105.1	P0C869-1
JMJD7-PLA2G4B	NM_005090.4 link	c.1398+49C>T	intron_variant		NP_005081.1	P0C869-6
JMJD7-PLA2G4B	NM_001198588.2 link	c.1398+49C>T	intron_variant		NP_001185517.1	P0C869-7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4B	ENST00000458483.4 link	c.705+49C>T		intron_variant		2	NM_001114633.2	ENSP00000416610.1		P0C869-1
JMJD7-PLA2G4B	ENST00000382448.8 link	c.1398+49C>T		intron_variant		2		ENSP00000371886.4

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

115261

AN:

151910

Hom.:

44381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.738

Gnomad AMR

AF:

0.818

Gnomad ASJ

AF:

0.884

Gnomad EAS

AF:

0.873

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.833

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.768

GnomAD3 exomes

AF:

0.804

AC:

194271

AN:

241764

Hom.:

78611

AF XY:

0.802

AC XY:

105496

AN XY:

131464

show subpopulations

Gnomad AFR exome

AF:

0.613

Gnomad AMR exome

AF:

0.847

Gnomad ASJ exome

AF:

0.877

Gnomad EAS exome

AF:

0.875

Gnomad SAS exome

AF:

0.739

Gnomad FIN exome

AF:

0.835

Gnomad NFE exome

AF:

0.811

Gnomad OTH exome

AF:

0.822

GnomAD4 exome

AF:

0.800

AC:

1165688

AN:

1456580

Hom.:

468203

Cov.:

AF XY:

0.799

AC XY:

579143

AN XY:

724424

show subpopulations

Gnomad4 AFR exome

AF:

0.604

Gnomad4 AMR exome

AF:

0.845

Gnomad4 ASJ exome

AF:

0.874

Gnomad4 EAS exome

AF:

0.883

Gnomad4 SAS exome

AF:

0.731

Gnomad4 FIN exome

AF:

0.834

Gnomad4 NFE exome

AF:

0.803

Gnomad4 OTH exome

AF:

0.809

GnomAD4 genome

AF:

0.759

AC:

115334

AN:

152028

Hom.:

44409

Cov.:

AF XY:

0.761

AC XY:

56546

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.617

Gnomad4 AMR

AF:

0.818

Gnomad4 ASJ

AF:

0.884

Gnomad4 EAS

AF:

0.873

Gnomad4 SAS

AF:

0.738

Gnomad4 FIN

AF:

0.833

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.772

Alfa

AF:

0.792

Hom.:

21192

Bravo

AF:

0.754

Asia WGS

AF:

0.810

AC:

2816

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.7

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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