Genetic Variant NAMPT-AS1:n.109C>T (chr7-106285307-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000609281.3(NAMPT-AS1):n.109C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 548,140 control chromosomes in the GnomAD database, including 158,965 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 0.77 ( 45168 hom., cov: 34)

Exomes 𝑓: 0.76 ( 113797 hom. )

Consequence

NAMPT-AS1
ENST00000609281.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.704

Publications

28 publications found

Variant links:

Genes affected

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

NAMPT-AS1 links:

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:

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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=-0.76).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAMPT-AS1	NR_186647.1 link	n.62C>T		non_coding_transcript_exon_variant	Exon 1 of 1
NAMPT	XM_047419699.1 link	c.-98+234G>A		intron_variant	Intron 1 of 11		XP_047275655.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
NAMPT-AS1	ENST00000609281.3 link	n.109C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
NAMPT	ENST00000424768.2 link	c.-98+234G>A	intron_variant	Intron 1 of 11	4	ENSP00000390591.2	P43490C9JG65
NAMPT	ENST00000681255.1 link	c.-48+234G>A	intron_variant	Intron 1 of 11		ENSP00000506129.1	P43490

Frequencies

GnomAD3 genomes

AF:

0.768

AC:

116661

AN:

151988

Hom.:

45113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.747

Gnomad AMR

AF:

0.823

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.879

Gnomad FIN

AF:

0.828

Gnomad MID

AF:

0.747

Gnomad NFE

AF:

0.759

Gnomad OTH

AF:

0.775

GnomAD4 exome

AF:

0.755

AC:

299050

AN:

396034

Hom.:

113797

Cov.:

AF XY:

0.756

AC XY:

141061

AN XY:

186574

show subpopulations

African (AFR)

AF:

0.691

AC:

5298

AN:

7672

American (AMR)

AF:

0.832

AC:

729

AN:

876

Ashkenazi Jewish (ASJ)

AF:

0.763

AC:

2262

AN:

2966

East Asian (EAS)

AF:

0.999

AC:

2840

AN:

2844

South Asian (SAS)

AF:

0.870

AC:

8128

AN:

9344

European-Finnish (FIN)

AF:

0.820

AC:

1100

AN:

1342

Middle Eastern (MID)

AF:

0.782

AC:

632

AN:

808

European-Non Finnish (NFE)

AF:

0.750

AC:

267372

AN:

356538

Other (OTH)

AF:

0.783

AC:

10689

AN:

13644

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3421

6842

10263

13684

17105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8608

17216

25824

34432

43040

<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:

0.768

AC:

116777

AN:

152106

Hom.:

45168

Cov.:

AF XY:

0.776

AC XY:

57674

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.705

AC:

29251

AN:

41508

American (AMR)

AF:

0.823

AC:

12598

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.768

AC:

2665

AN:

3470

East Asian (EAS)

AF:

0.999

AC:

5143

AN:

5150

South Asian (SAS)

AF:

0.879

AC:

4241

AN:

4824

European-Finnish (FIN)

AF:

0.828

AC:

8777

AN:

10602

Middle Eastern (MID)

AF:

0.755

AC:

222

AN:

294

European-Non Finnish (NFE)

AF:

0.759

AC:

51555

AN:

67934

Other (OTH)

AF:

0.778

AC:

1644

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1424

2848

4273

5697

7121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.762

Hom.:

27533

Bravo

AF:

0.763

Asia WGS

AF:

0.937

AC:

3261

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.0

(source)

DANN

Benign

0.90

PhyloP100

-0.70

PromoterAI

-0.13

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over