NM_001122838.3:c.1057-2077T>G

Variant names:

• chr7-103105631-A-C
• rs11487077
• NM_001122838.3:c.1057-2077T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001122838.3(NAPEPLD):​c.1057-2077T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 152,250 control chromosomes in the GnomAD database, including 356 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 0.065 (356 hom., cov: 33)
• Consequence: NAPEPLD NM_001122838.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAPEPLD	NM_001122838.3	c.1057-2077T>G		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.1057-2077T>G		intron_variant	Intron 4 of 4	1	NM_001122838.3	ENSP00000419188.1

Frequencies

GnomAD3 genomes AF: 0.0648 AC: 9857 AN: 152132 Hom.: 357 Cov.: 33

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0647 AC: 9856 AN: 152250 Hom.: 356 Cov.: 33 AF XY: 0.0625 AC XY: 4655 AN XY: 74458

African (AFR) AF: 0.0559 AC: 2323 AN: 41554

American (AMR) AF: 0.0630 AC: 964 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0499 AC: 241 AN: 4830

European-Finnish (FIN) AF: 0.0473 AC: 502 AN: 10604

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0781 AC: 5310 AN: 67988

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0717 Hom.: 571

Bravo AF: 0.0653

Asia WGS AF: 0.0270 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.62
PhyloP100		0.35
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: rs11487077; hg19: chr7-102746078;