7-106283804-T-C

Variant names:

• chr7-106283804-T-C
• rs3801266
• NM_005746.3:c.57+1024A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005746.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT	NM_005746.3	MANE Select	c.57+1024A>G		intron	N/A	NP_005737.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT	ENST00000222553.8	TSL:1 MANE Select	c.57+1024A>G		intron	N/A	ENSP00000222553.3
	NAMPT	ENST00000354289.9	TSL:1	c.57+1024A>G		intron	N/A	ENSP00000346242.4
	NAMPT	ENST00000424768.2	TSL:4	c.57+1024A>G		intron	N/A	ENSP00000390591.2

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

African (AFR) AF: 0.465 AC: 19218 AN: 41360

American (AMR) AF: 0.176 AC: 2694 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.108 AC: 560 AN: 5176

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4802

European-Finnish (FIN) AF: 0.149 AC: 1571 AN: 10552

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12645 AN: 67932

Other (OTH) AF: 0.255 AC: 538 AN: 2106

Alfa AF: 0.209 Hom.: 4902

Bravo AF: 0.267

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3801266; hg19: chr7-105924250;