Genetic Variant NAMPT:c.744-87T>C (chr7-106263704-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005746.3(NAMPT):c.744-87T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 967,860 control chromosomes in the GnomAD database, including 172,642 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 ( 22164 hom., cov: 32)

Exomes 𝑓: 0.60 ( 150478 hom. )

Consequence

NAMPT
NM_005746.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.804

Publications

25 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:

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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
NAMPT	NM_005746.3 link	c.744-87T>C	intron_variant	Intron 6 of 10	ENST00000222553.8	NP_005737.1	P43490A0A024R718
NAMPT	XM_047419700.1 link	c.*1449T>C	3_prime_UTR_variant	Exon 7 of 7		XP_047275656.1
NAMPT	XM_047419699.1 link	c.744-87T>C	intron_variant	Intron 7 of 11		XP_047275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAMPT	ENST00000222553.8 link	c.744-87T>C		intron_variant	Intron 6 of 10	1	NM_005746.3	ENSP00000222553.3		P43490

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76520

AN:

151750

Hom.:

22147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.652

Gnomad ASJ

AF:

0.516

Gnomad EAS

AF:

0.893

Gnomad SAS

AF:

0.659

Gnomad FIN

AF:

0.688

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.520

GnomAD4 exome

AF:

0.597

AC:

487407

AN:

815992

Hom.:

150478

AF XY:

0.600

AC XY:

255350

AN XY:

425692

show subpopulations

African (AFR)

AF:

0.203

AC:

4049

AN:

19964

American (AMR)

AF:

0.744

AC:

27075

AN:

36408

Ashkenazi Jewish (ASJ)

AF:

0.509

AC:

9423

AN:

18512

East Asian (EAS)

AF:

0.899

AC:

32855

AN:

36528

South Asian (SAS)

AF:

0.649

AC:

41695

AN:

64278

European-Finnish (FIN)

AF:

0.672

AC:

33594

AN:

49998

Middle Eastern (MID)

AF:

0.500

AC:

2157

AN:

4312

European-Non Finnish (NFE)

AF:

0.575

AC:

314559

AN:

547428

Other (OTH)

AF:

0.570

AC:

22000

AN:

38564

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

9713

19426

29138

38851

48564

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5886

11772

17658

23544

29430

<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:

0.504

AC:

76559

AN:

151868

Hom.:

22164

Cov.:

AF XY:

0.519

AC XY:

38524

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.212

AC:

8782

AN:

41448

American (AMR)

AF:

0.653

AC:

9953

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.516

AC:

1785

AN:

3460

East Asian (EAS)

AF:

0.894

AC:

4624

AN:

5174

South Asian (SAS)

AF:

0.660

AC:

3179

AN:

4820

European-Finnish (FIN)

AF:

0.688

AC:

7279

AN:

10578

Middle Eastern (MID)

AF:

0.493

AC:

144

AN:

292

European-Non Finnish (NFE)

AF:

0.577

AC:

39153

AN:

67844

Other (OTH)

AF:

0.524

AC:

1104

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1662

3324

4987

6649

8311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.510

Hom.:

3132

Bravo

AF:

0.493

Asia WGS

AF:

0.721

AC:

2508

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.8

(source)

DANN

Benign

0.78

PhyloP100

0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over