rs17605251

chr7-103105504-A-G

Variant summary

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

The NM_001122838.3(NAPEPLD):c.1057-1950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 152,330 control chromosomes in the GnomAD database, including 687 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 0.082 (687 hom., cov: 33)
• Consequence: NAPEPLD NM_001122838.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAPEPLD	NM_001122838.3	c.1057-1950T>C		intron_variant		ENST00000465647.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAPEPLD	ENST00000465647.6	c.1057-1950T>C		intron_variant		1	NM_001122838.3	P1

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12496 AN: 152212 Hom.: 687 Cov.: 33

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0821 AC: 12499 AN: 152330 Hom.: 687 Cov.: 33 AF XY: 0.0841 AC XY: 6262 AN XY: 74482

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.105 Hom.: 1184

Bravo AF: 0.0740

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.9
Dann	Benign	0.61

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: rs17605251; hg19: chr7-102745951;