rs6465903

Variant names:

• chr7-103134811-C-A
• rs6465903
• NM_001122838.3:c.-16-6019G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122838.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAPEPLD	NM_001122838.3	MANE Select	c.-16-6019G>T		intron	N/A	NP_001116310.1	Q6IQ20
	NAPEPLD	NM_001386176.1		c.-16-6019G>T		intron	N/A	NP_001373105.1	Q6IQ20
	NAPEPLD	NM_001386177.1		c.-16-6019G>T		intron	N/A	NP_001373106.1	Q6IQ20

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAPEPLD	ENST00000465647.6	TSL:1 MANE Select	c.-16-6019G>T		intron	N/A	ENSP00000419188.1	Q6IQ20
	NAPEPLD	ENST00000341533.8	TSL:1	c.-16-6019G>T		intron	N/A	ENSP00000340093.4	Q6IQ20
	NAPEPLD	ENST00000422589.5	TSL:1	n.-16-6019G>T		intron	N/A	ENSP00000412376.1	Q6IQ20

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

African (AFR) AF: 0.170 AC: 7037 AN: 41464

American (AMR) AF: 0.111 AC: 1689 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3468

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.111 AC: 535 AN: 4822

European-Finnish (FIN) AF: 0.0829 AC: 875 AN: 10552

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9165 AN: 68010

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.145 Hom.: 281

Bravo AF: 0.135

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.11
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: rs6465903; hg19: chr7-102775258;