15-42070623-C-G

Position:

• chr15-42070623-C-G

Variant summary

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

The NM_178034.4(PLA2G4D):​c.2043+94G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 1,377,950 control chromosomes in the GnomAD database, including 450,987 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 0.80 (49304 hom., cov: 33)
  • Exomes 𝑓: 0.81 (401683 hom.)
• Consequence: PLA2G4D NM_178034.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

Genes affected

PLA2G4D (HGNC:30038): (phospholipase A2 group IVD) The phospholipase A2 enzyme family, including PLA2G4D, catalyze the hydrolysis of glycerophospholipids at the sn-2 position and then liberate free fatty acids and lysophospholipids (Chiba et al., 2004 [PubMed 14709560]).[supplied by OMIM, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G4D	NM_178034.4	c.2043+94G>C		intron_variant		ENST00000290472.4
PLA2G4D	XM_047432399.1	c.2043+94G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G4D	ENST00000290472.4	c.2043+94G>C		intron_variant		1	NM_178034.4	P1
PLA2G4D	ENST00000560932.1	n.669G>C		non_coding_transcript_exon_variant	4/5	1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122263 AN: 152066 Hom.: 49265 Cov.: 33

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.806

GnomAD4 exome AF: 0.809 AC: 991095 AN: 1225766 Hom.: 401683 Cov.: 19 AF XY: 0.805 AC XY: 483430 AN XY: 600670

Gnomad4 AFR exome AF: 0.787

Gnomad4 AMR exome AF: 0.869

Gnomad4 ASJ exome AF: 0.695

Gnomad4 EAS exome AF: 0.791

Gnomad4 SAS exome AF: 0.685

Gnomad4 FIN exome AF: 0.811

Gnomad4 NFE exome AF: 0.820

Gnomad4 OTH exome AF: 0.793

GnomAD4 genome AF: 0.804 AC: 122360 AN: 152184 Hom.: 49304 Cov.: 33 AF XY: 0.802 AC XY: 59652 AN XY: 74386

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.804

Alfa AF: 0.745 Hom.: 2266

Bravo AF: 0.812

Asia WGS AF: 0.768 AC: 2671 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
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: rs2459692; hg19: chr15-42362821;