15-42044519-G-T

Position:

• chr15-42044519-G-T

Variant summary

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

The XR_932177.1(LOC105370793):​n.740G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 151,718 control chromosomes in the GnomAD database, including 594 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 0.087 (594 hom., cov: 28)
• Consequence: LOC105370793 XR_932177.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

LOC105370793 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370793	XR_932177.1	n.740G>T		non_coding_transcript_exon_variant	3/3
PLA2G4E	NM_001206670.1	c.183+6002C>A		intron_variant			NP_001193599.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G4E	ENST00000399518.3	c.183+6002C>A		intron_variant		5		ENSP00000382434	P2
PLA2G4E	ENST00000696117.1	c.-17+5021C>A		intron_variant, NMD_transcript_variant				ENSP00000512411

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13133 AN: 151600 Hom.: 594 Cov.: 28

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.101

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0866 AC: 13142 AN: 151718 Hom.: 594 Cov.: 28 AF XY: 0.0872 AC XY: 6458 AN XY: 74088

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0709

Gnomad4 NFE AF: 0.0657

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0749 Hom.: 659

Bravo AF: 0.0871

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.39

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: rs7176475; hg19: chr15-42336717;