rs1668565

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-42013800-T-A
• chr15-42013800-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001206670.1(PLA2G4E):​c.184-43A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000074 in 1,351,794 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 28)
  • Exomes 𝑓: 7.4e-7 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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>T		intron	N/A	NP_001382477.1
	PLA2G4E	NM_001206670.1		c.184-43A>T		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>T		intron	N/A	ENSP00000512406.1
	PLA2G4E	ENST00000399518.3	TSL:5	c.184-43A>T		intron	N/A	ENSP00000382434.3
	PLA2G4E	ENST00000696114.1		n.97-43A>T		intron	N/A	ENSP00000512408.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 7.40e-7 AC: 1 AN: 1351794 Hom.: 0 Cov.: 24 AF XY: 0.00000150 AC XY: 1 AN XY: 668828

African (AFR) AF: 0.00 AC: 0 AN: 30468

American (AMR) AF: 0.00 AC: 0 AN: 35372

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24584

East Asian (EAS) AF: 0.00 AC: 0 AN: 35460

South Asian (SAS) AF: 0.00 AC: 0 AN: 78254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45208

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5548

European-Non Finnish (NFE) AF: 9.61e-7 AC: 1 AN: 1040594

Other (OTH) AF: 0.00 AC: 0 AN: 56306

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		-0.56

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;