dbSNP rs61330082: NAMPT:c.-272-654C>T (chr7-106286419-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000901886.1(NAMPT):c.-272-654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,176 control chromosomes in the GnomAD database, including 4,697 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 0.23 ( 4695 hom., cov: 33)

Exomes 𝑓: 0.40 ( 2 hom. )

Consequence

NAMPT
ENST00000901886.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.191

Publications

50 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:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000901886.1. 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.*93G>A		downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NAMPT	ENST00000901886.1		c.-272-654C>T	intron	N/A	ENSP00000571945.1
NAMPT	ENST00000901887.1		c.-322-654C>T	intron	N/A	ENSP00000571946.1
NAMPT-AS1	ENST00000609281.3	TSL:6	n.*93G>A	downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34978

AN:

152036

Hom.:

4689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.247

GnomAD4 exome

AF:

0.400

AC:

AN:

Hom.:

AF XY:

0.313

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.230

AC:

35005

AN:

152156

Hom.:

4695

Cov.:

AF XY:

0.236

AC XY:

17574

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.107

AC:

4451

AN:

41542

American (AMR)

AF:

0.323

AC:

4944

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

908

AN:

3470

East Asian (EAS)

AF:

0.487

AC:

2521

AN:

5180

South Asian (SAS)

AF:

0.256

AC:

1235

AN:

4830

European-Finnish (FIN)

AF:

0.305

AC:

3216

AN:

10550

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.249

AC:

16942

AN:

67976

Other (OTH)

AF:

0.252

AC:

532

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1351

2702

4053

5404

6755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

370

740

1110

1480

1850

<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:

0.241

Hom.:

6354

Bravo

AF:

0.229

Asia WGS

AF:

0.372

AC:

1291

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.4

(source)

DANN

Benign

0.60

PhyloP100

-0.19

PromoterAI

-0.015

Neutral

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over