dbSNP rs41430346: NAMPT:c.319-51G>C (chr7-106272709-C-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.319-51G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,594,120 control chromosomes in the GnomAD database, including 423 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 0.028 ( 91 hom., cov: 32)

Exomes 𝑓: 0.018 ( 332 hom. )

Consequence

NAMPT
NM_005746.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.125

Publications

5 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
NAMPT	NM_005746.3 link	c.319-51G>C	intron_variant	Intron 3 of 10	ENST00000222553.8	NP_005737.1
NAMPT	XM_047419699.1 link	c.319-51G>C	intron_variant	Intron 4 of 11		XP_047275655.1
NAMPT	XM_047419700.1 link	c.319-51G>C	intron_variant	Intron 3 of 6		XP_047275656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAMPT	ENST00000222553.8 link	c.319-51G>C		intron_variant	Intron 3 of 10	1	NM_005746.3	ENSP00000222553.3

Frequencies

GnomAD3 genomes

AF:

0.0275

AC:

4187

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0586

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0190

Gnomad ASJ

AF:

0.0219

Gnomad EAS

AF:

0.0169

Gnomad SAS

AF:

0.00993

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0170

Gnomad OTH

AF:

0.0268

GnomAD2 exomes

AF:

0.0195

AC:

4770

AN:

245078

AF XY:

0.0185

show subpopulations

Gnomad AFR exome

AF:

0.0622

Gnomad AMR exome

AF:

0.0168

Gnomad ASJ exome

AF:

0.0201

Gnomad EAS exome

AF:

0.0162

Gnomad FIN exome

AF:

0.00546

Gnomad NFE exome

AF:

0.0197

Gnomad OTH exome

AF:

0.0266

GnomAD4 exome

AF:

0.0184

AC:

26585

AN:

1441910

Hom.:

332

Cov.:

AF XY:

0.0181

AC XY:

12991

AN XY:

718200

show subpopulations

African (AFR)

AF:

0.0621

AC:

2028

AN:

32676

American (AMR)

AF:

0.0186

AC:

806

AN:

43330

Ashkenazi Jewish (ASJ)

AF:

0.0189

AC:

483

AN:

25498

East Asian (EAS)

AF:

0.0131

AC:

517

AN:

39344

South Asian (SAS)

AF:

0.0107

AC:

908

AN:

84686

European-Finnish (FIN)

AF:

0.00602

AC:

318

AN:

52822

Middle Eastern (MID)

AF:

0.0127

AC:

AN:

5684

European-Non Finnish (NFE)

AF:

0.0184

AC:

20190

AN:

1098412

Other (OTH)

AF:

0.0212

AC:

1263

AN:

59458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

1082

2163

3245

4326

5408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.0275

AC:

4190

AN:

152210

Hom.:

Cov.:

AF XY:

0.0264

AC XY:

1966

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0585

AC:

2430

AN:

41518

American (AMR)

AF:

0.0189

AC:

289

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0219

AC:

AN:

3464

East Asian (EAS)

AF:

0.0170

AC:

AN:

5188

South Asian (SAS)

AF:

0.00994

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00443

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0170

AC:

1154

AN:

67996

Other (OTH)

AF:

0.0265

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

198

396

595

793

991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0229

Hom.:

Bravo

AF:

0.0299

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.9

(source)

DANN

Benign

0.47

PhyloP100

0.13

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