rs6465903

Positions:

• chr7-103134811-C-A

Variant summary

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

The NM_001122838.3(NAPEPLD):​c.-16-6019G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,104 control chromosomes in the GnomAD database, including 1,413 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 0.13 (1413 hom., cov: 33)
• Consequence: NAPEPLD NM_001122838.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

NAPEPLD (HGNC:21683): (N-acyl phosphatidylethanolamine phospholipase D) NAPEPLD is a phospholipase D type enzyme that catalyzes the release of N-acylethanolamine (NAE) from N-acyl-phosphatidylethanolamine (NAPE) in the second step of the biosynthesis of N-acylethanolamine (Okamoto et al., 2004 [PubMed 14634025]).[supplied by OMIM, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAPEPLD	NM_001122838.3	c.-16-6019G>T		intron_variant		ENST00000465647.6	NP_001116310.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAPEPLD	ENST00000465647.6	c.-16-6019G>T		intron_variant		1	NM_001122838.3	ENSP00000419188	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20211 AN: 151986 Hom.: 1410 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.133 AC: 20223 AN: 152104 Hom.: 1413 Cov.: 33 AF XY: 0.129 AC XY: 9629 AN XY: 74358

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.141

Alfa AF: 0.143 Hom.: 262

Bravo AF: 0.135

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.6
DANN	Benign	0.68

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: rs6465903; hg19: chr7-102775258;