dbSNP rs9770242: NAMPT:c.-442G>T (chr7-106285885-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000424768.2(NAMPT):c.-442G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,160 control chromosomes in the GnomAD database, including 47,595 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 0.79 ( 47573 hom., cov: 31)

Exomes 𝑓: 0.75 ( 22 hom. )

Consequence

NAMPT
ENST00000424768.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.421

Publications

41 publications found

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]

NAMPT links:

NAMPT-AS1 (HGNC:56696): (NAMPT antisense RNA 1)

NAMPT-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424768.2. 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-AS1	NR_186647.1		n.640C>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NAMPT	ENST00000424768.2	TSL:4	c.-442G>T	5_prime_UTR	Exon 1 of 12	ENSP00000390591.2	P43490
NAMPT	ENST00000681255.1		c.-392G>T	5_prime_UTR	Exon 1 of 12	ENSP00000506129.1	P43490
NAMPT	ENST00000901886.1		c.-272-120G>T	intron	N/A	ENSP00000571945.1

Frequencies

GnomAD3 genomes

AF:

0.789

AC:

119881

AN:

151966

Hom.:

47521

Cov.:

show subpopulations

Gnomad AFR

AF:

0.779

Gnomad AMI

AF:

0.747

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.880

Gnomad FIN

AF:

0.828

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.760

Gnomad OTH

AF:

0.789

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.795

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

0.800

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.789

AC:

119996

AN:

152084

Hom.:

47573

Cov.:

AF XY:

0.796

AC XY:

59186

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.779

AC:

32292

AN:

41456

American (AMR)

AF:

0.827

AC:

12637

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.768

AC:

2661

AN:

3464

East Asian (EAS)

AF:

0.999

AC:

5174

AN:

5180

South Asian (SAS)

AF:

0.880

AC:

4240

AN:

4816

European-Finnish (FIN)

AF:

0.828

AC:

8770

AN:

10594

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.760

AC:

51643

AN:

67970

Other (OTH)

AF:

0.792

AC:

1675

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1288

2577

3865

5154

6442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

872

1744

2616

3488

4360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.785

Hom.:

27825

Bravo

AF:

0.789

Asia WGS

AF:

0.944

AC:

3285

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.8

(source)

DANN

Benign

0.84

PhyloP100

-0.42

PromoterAI

-0.075

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over