rs2058539

Positions:

• chr7-106276191-C-A
• chr7-106276191-C-G
• chr7-106276191-C-T

Variant summary

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

The NM_005746.3(NAMPT):​c.214+832G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,040 control chromosomes in the GnomAD database, including 29,127 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 0.61 (29127 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: NAMPT NM_005746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAMPT	NM_005746.3	c.214+832G>T		intron_variant		ENST00000222553.8
NAMPT	XM_047419699.1	c.214+832G>T		intron_variant
NAMPT	XM_047419700.1	c.214+832G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAMPT	ENST00000222553.8	c.214+832G>T		intron_variant		1	NM_005746.3	P4

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93212 AN: 151922 Hom.: 29091 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.625

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.614 AC: 93314 AN: 152040 Hom.: 29127 Cov.: 32 AF XY: 0.626 AC XY: 46484 AN XY: 74300

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.629

Alfa AF: 0.557 Hom.: 3215

Bravo AF: 0.615

Asia WGS AF: 0.754 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058539; hg19: chr7-105916637;