chr7-106283697-T-C

Position:

• chr7-106283697-T-C

Variant summary

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

The ENST00000222553.8(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 ENST00000222553.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAMPT	NM_005746.3	c.57+1131A>G		intron_variant		ENST00000222553.8	NP_005737.1
NAMPT	XM_047419699.1	c.57+1131A>G		intron_variant			XP_047275655.1
NAMPT	XM_047419700.1	c.57+1131A>G		intron_variant			XP_047275656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAMPT	ENST00000222553.8	c.57+1131A>G		intron_variant		1	NM_005746.3	ENSP00000222553	P4

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

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.522

Alfa AF: 0.465 Hom.: 2397

Bravo AF: 0.492

Asia WGS AF: 0.716 AC: 2491 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.55

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: rs4730155; hg19: chr7-105924143;