chr7-106251985-C-T

Variant names:

• chr7-106251985-C-T
• rs10953502
• NM_005746.3:c.1366-792G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005746.3(NAMPT):​c.1366-792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 143,604 control chromosomes in the GnomAD database, including 24,427 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 0.58 (24427 hom., cov: 31)
• Consequence: NAMPT NM_005746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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.1366-792G>A		intron	N/A	NP_005737.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT	ENST00000222553.8	TSL:1 MANE Select	c.1366-792G>A		intron	N/A	ENSP00000222553.3
	NAMPT	ENST00000463871.2	TSL:1	n.4462-792G>A		intron	N/A
	NAMPT	ENST00000680468.1		c.*1002G>A		3_prime_UTR	Exon 10 of 10	ENSP00000505172.1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 83513 AN: 143504 Hom.: 24404 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.582 AC: 83595 AN: 143604 Hom.: 24427 Cov.: 31 AF XY: 0.594 AC XY: 41799 AN XY: 70364

African (AFR) AF: 0.437 AC: 14582 AN: 33376

American (AMR) AF: 0.693 AC: 10432 AN: 15062

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2038 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4608 AN: 5176

South Asian (SAS) AF: 0.621 AC: 2997 AN: 4826

European-Finnish (FIN) AF: 0.692 AC: 7312 AN: 10570

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39688 AN: 67842

Other (OTH) AF: 0.589 AC: 1224 AN: 2078

Alfa AF: 0.575 Hom.: 3041

Bravo AF: 0.602

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.37
PhyloP100		-1.7
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: rs10953502; hg19: chr7-105892431;