NM_001122838.3:c.1057-1950T>C

Variant names:

• chr7-103105504-A-G
• rs17605251
• NM_001122838.3:c.1057-1950T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NAPEPLD	NM_001122838.3	c.1057-1950T>C		intron_variant	Intron 4 of 4	ENST00000465647.6	NP_001116310.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAPEPLD	ENST00000465647.6	c.1057-1950T>C		intron_variant	Intron 4 of 4	1	NM_001122838.3	ENSP00000419188.1

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

African (AFR) AF: 0.0211 AC: 877 AN: 41590

American (AMR) AF: 0.0904 AC: 1384 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5186

South Asian (SAS) AF: 0.161 AC: 777 AN: 4826

European-Finnish (FIN) AF: 0.110 AC: 1167 AN: 10610

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7252 AN: 68024

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0954 Hom.: 1605

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
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs17605251; hg19: chr7-102745951;