chr15-42013800-T-C

Variant names:

• chr15-42013800-T-C
• rs1668565
• NM_001395548.1:c.97-43A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001206670.1(PLA2G4E):​c.184-43A>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_001206670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001206670.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4E	NM_001395548.1	MANE Select	c.97-43A>G		intron	N/A	NP_001382477.1
	PLA2G4E	NM_001206670.1		c.184-43A>G		intron	N/A	NP_001193599.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4E	ENST00000696112.1	MANE Select	c.97-43A>G		intron	N/A	ENSP00000512406.1
	PLA2G4E	ENST00000399518.3	TSL:5	c.184-43A>G		intron	N/A	ENSP00000382434.3
	PLA2G4E	ENST00000696114.1		n.97-43A>G		intron	N/A	ENSP00000512408.1

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

GnomAD2 exomes AF: 0.608 AC: 86487 AN: 142214 AF XY: 0.609

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 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

African (AFR) AF: 0.488 AC: 14860 AN: 30426

American (AMR) AF: 0.529 AC: 18699 AN: 35344

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 12730 AN: 24560

East Asian (EAS) AF: 0.829 AC: 29374 AN: 35450

South Asian (SAS) AF: 0.578 AC: 45199 AN: 78196

European-Finnish (FIN) AF: 0.590 AC: 26607 AN: 45094

Middle Eastern (MID) AF: 0.552 AC: 3063 AN: 5544

European-Non Finnish (NFE) AF: 0.626 AC: 650802 AN: 1039368

Other (OTH) AF: 0.615 AC: 34610 AN: 56246

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

African (AFR) AF: 0.498 AC: 20003 AN: 40160

American (AMR) AF: 0.547 AC: 8096 AN: 14794

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1695 AN: 3386

East Asian (EAS) AF: 0.799 AC: 4075 AN: 5102

South Asian (SAS) AF: 0.634 AC: 2872 AN: 4530

European-Finnish (FIN) AF: 0.622 AC: 6018 AN: 9680

Middle Eastern (MID) AF: 0.587 AC: 162 AN: 276

European-Non Finnish (NFE) AF: 0.644 AC: 42045 AN: 65292

Other (OTH) AF: 0.593 AC: 1209 AN: 2038

Alfa AF: 0.599 Hom.: 47777

Bravo AF: 0.570

Asia WGS AF: 0.680 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1668565; hg19: chr15-42305998;