rs2058539

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.567
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
NAMPTNM_005746.3 linkuse as main transcriptc.214+832G>T intron_variant ENST00000222553.8
NAMPTXM_047419699.1 linkuse as main transcriptc.214+832G>T intron_variant
NAMPTXM_047419700.1 linkuse as main transcriptc.214+832G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAMPTENST00000222553.8 linkuse as main transcriptc.214+832G>T intron_variant 1 NM_005746.3 P4

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2058539; hg19: chr7-105916637; API