7-106283697-T-C

Variant names:

• chr7-106283697-T-C
• rs4730155
• NM_005746.3:c.57+1131A>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+1131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,064 control chromosomes in the GnomAD database, including 22,174 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 0.50 (22174 hom., cov: 32)
• Consequence: NAMPT NM_005746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT	NM_005746.3	MANE Select	c.57+1131A>G		intron	N/A	NP_005737.1	P43490

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT	ENST00000222553.8	TSL:1 MANE Select	c.57+1131A>G		intron	N/A	ENSP00000222553.3	P43490
	NAMPT	ENST00000354289.9	TSL:1	c.57+1131A>G		intron	N/A	ENSP00000346242.4	A0A0C4DFS8
	NAMPT	ENST00000968694.1		c.57+1131A>G		intron	N/A	ENSP00000638753.1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76583 AN: 151946 Hom.: 22156 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.504 AC: 76624 AN: 152064 Hom.: 22174 Cov.: 32 AF XY: 0.519 AC XY: 38582 AN XY: 74358

African (AFR) AF: 0.211 AC: 8774 AN: 41490

American (AMR) AF: 0.653 AC: 9980 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4610 AN: 5174

South Asian (SAS) AF: 0.658 AC: 3175 AN: 4824

European-Finnish (FIN) AF: 0.689 AC: 7277 AN: 10564

Middle Eastern (MID) AF: 0.493 AC: 143 AN: 290

European-Non Finnish (NFE) AF: 0.577 AC: 39200 AN: 67944

Other (OTH) AF: 0.522 AC: 1105 AN: 2116

Alfa AF: 0.454 Hom.: 2410

Bravo AF: 0.492

Asia WGS AF: 0.716 AC: 2491 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.55
PhyloP100		0.22
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: rs4730155; hg19: chr7-105924143;