chr7-106278476-A-T

Variant names:

• chr7-106278476-A-T
• rs3801267
• NM_005746.3:c.58-1297T>A

Variant summary

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

The NM_005746.3(NAMPT):​c.58-1297T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,908 control chromosomes in the GnomAD database, including 31,791 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 0.64 (31791 hom., cov: 31)
• Consequence: NAMPT NM_005746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAMPT	NM_005746.3	c.58-1297T>A		intron_variant	Intron 1 of 10	ENST00000222553.8	NP_005737.1
NAMPT	XM_047419699.1	c.58-1297T>A		intron_variant	Intron 2 of 11		XP_047275655.1
NAMPT	XM_047419700.1	c.58-1297T>A		intron_variant	Intron 1 of 6		XP_047275656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAMPT	ENST00000222553.8	c.58-1297T>A		intron_variant	Intron 1 of 10	1	NM_005746.3	ENSP00000222553.3

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97580 AN: 151790 Hom.: 31752 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.643 AC: 97686 AN: 151908 Hom.: 31791 Cov.: 31 AF XY: 0.655 AC XY: 48586 AN XY: 74228

African (AFR) AF: 0.575 AC: 23812 AN: 41400

American (AMR) AF: 0.739 AC: 11293 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2166 AN: 3468

East Asian (EAS) AF: 0.910 AC: 4708 AN: 5172

South Asian (SAS) AF: 0.689 AC: 3319 AN: 4820

European-Finnish (FIN) AF: 0.732 AC: 7715 AN: 10542

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42535 AN: 67910

Other (OTH) AF: 0.658 AC: 1390 AN: 2112

Alfa AF: 0.620 Hom.: 3660

Bravo AF: 0.645

Asia WGS AF: 0.776 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.75
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: rs3801267; hg19: chr7-105918922;