15-42013800-T-C

Position:

• chr15-42013800-T-C

Variant summary

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

The NM_001395548.1(PLA2G4E):​c.97-43A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 1,496,386 control chromosomes in the GnomAD database, including 286,102 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 0.59 (25479 hom., cov: 28)
  • Exomes 𝑓: 0.62 (260623 hom.)
• Consequence: PLA2G4E NM_001395548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

PLA2G4E (HGNC:24791): (phospholipase A2 group IVE) This gene encodes a member of the cytosolic phospholipase A2 group IV family. Members of this family are involved in regulation of membrane tubule-mediated transport. The enzyme encoded by this member of the family plays a role in trafficking through the clathrin-independent endocytic pathway. The enzyme regulates the recycling process via formation of tubules that transport internalized clathrin-independent cargo proteins back to the cell surface. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G4E	NM_001395548.1	c.97-43A>G		intron_variant		ENST00000696112.1	NP_001382477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4E	ENST00000696112.1	c.97-43A>G		intron_variant			NM_001395548.1	ENSP00000512406	A2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 86820 AN: 146064 Hom.: 25457 Cov.: 28

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.589

GnomAD3 exomes AF: 0.608 AC: 86487 AN: 142214 Hom.: 26257 AF XY: 0.609 AC XY: 46768 AN XY: 76736

Gnomad AFR exome AF: 0.485

Gnomad AMR exome AF: 0.532

Gnomad ASJ exome AF: 0.521

Gnomad EAS exome AF: 0.812

Gnomad SAS exome AF: 0.597

Gnomad FIN exome AF: 0.614

Gnomad NFE exome AF: 0.634

Gnomad OTH exome AF: 0.605

GnomAD4 exome AF: 0.619 AC: 835944 AN: 1350228 Hom.: 260623 Cov.: 24 AF XY: 0.618 AC XY: 412632 AN XY: 668164

Gnomad4 AFR exome AF: 0.488

Gnomad4 AMR exome AF: 0.529

Gnomad4 ASJ exome AF: 0.518

Gnomad4 EAS exome AF: 0.829

Gnomad4 SAS exome AF: 0.578

Gnomad4 FIN exome AF: 0.590

Gnomad4 NFE exome AF: 0.626

Gnomad4 OTH exome AF: 0.615

GnomAD4 genome AF: 0.594 AC: 86884 AN: 146158 Hom.: 25479 Cov.: 28 AF XY: 0.593 AC XY: 42258 AN XY: 71226

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.593

Alfa AF: 0.603 Hom.: 38621

Bravo AF: 0.570

Asia WGS AF: 0.680 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs1668565; hg19: chr15-42305998;