rs3801266

Positions:

• chr7-106283804-T-C

Variant summary

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

The NM_005746.3(NAMPT):​c.57+1024A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,884 control chromosomes in the GnomAD database, including 6,338 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 0.26 (6338 hom., cov: 32)
• Consequence: NAMPT NM_005746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

NAMPT (HGNC:30092): (nicotinamide phosphoribosyltransferase) This gene encodes a protein that catalyzes the condensation of nicotinamide with 5-phosphoribosyl-1-pyrophosphate to yield nicotinamide mononucleotide, one step in the biosynthesis of nicotinamide adenine dinucleotide. The protein belongs to the nicotinic acid phosphoribosyltransferase (NAPRTase) family and is thought to be involved in many important biological processes, including metabolism, stress response and aging. This gene has a pseudogene on chromosome 10. [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAMPT	NM_005746.3	c.57+1024A>G		intron_variant		ENST00000222553.8	NP_005737.1
NAMPT	XM_047419699.1	c.57+1024A>G		intron_variant			XP_047275655.1
NAMPT	XM_047419700.1	c.57+1024A>G		intron_variant			XP_047275656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAMPT	ENST00000222553.8	c.57+1024A>G		intron_variant		1	NM_005746.3	ENSP00000222553.3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39306 AN: 151764 Hom.: 6317 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.259 AC: 39366 AN: 151884 Hom.: 6338 Cov.: 32 AF XY: 0.253 AC XY: 18806 AN XY: 74248

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.255

Alfa AF: 0.200 Hom.: 3321

Bravo AF: 0.267

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs3801266; hg19: chr7-105924250;