dbSNP rs12678314: NAPRT:c.438-39T>C (chr8-143577438-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_145201.6(NAPRT):c.438-39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 1,580,642 control chromosomes in the GnomAD database, including 440,218 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 0.72 ( 40220 hom., cov: 35)

Exomes 𝑓: 0.75 ( 399998 hom. )

Consequence

NAPRT
NM_145201.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.761

Publications

12 publications found

Variant links:

Genes affected

NAPRT (HGNC:30450): (nicotinate phosphoribosyltransferase) Nicotinic acid (NA; niacin) is converted by nicotinic acid phosphoribosyltransferase (NAPRT; EC 2.4.2.11) to NA mononucleotide (NaMN), which is then converted to NA adenine dinucleotide (NaAD), and finally to nicotinamide adenine dinucleotide (NAD), which serves as a coenzyme in cellular redox reactions and is an essential component of a variety of processes in cellular metabolism including response to stress (Hara et al., 2007).[supplied by OMIM, Mar 2008]

NAPRT links:

ENSG00000255050 (HGNC:):

ENSG00000255050 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAPRT	NM_145201.6 link	c.438-39T>C		intron_variant	Intron 3 of 12	ENST00000449291.7	NP_660202.3	Q6XQN6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAPRT	ENST00000449291.7 link	c.438-39T>C		intron_variant	Intron 3 of 12	1	NM_145201.6	ENSP00000401508.2		Q6XQN6-1

Frequencies

GnomAD3 genomes

AF:

0.725

AC:

110214

AN:

152044

Hom.:

40193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.742

Gnomad AMR

AF:

0.744

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.622

Gnomad FIN

AF:

0.709

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.766

Gnomad OTH

AF:

0.711

GnomAD2 exomes

AF:

0.722

AC:

148671

AN:

205854

AF XY:

0.718

show subpopulations

Gnomad AFR exome

AF:

0.657

Gnomad AMR exome

AF:

0.739

Gnomad ASJ exome

AF:

0.661

Gnomad EAS exome

AF:

0.738

Gnomad FIN exome

AF:

0.708

Gnomad NFE exome

AF:

0.760

Gnomad OTH exome

AF:

0.716

GnomAD4 exome

AF:

0.747

AC:

1067151

AN:

1428480

Hom.:

399998

Cov.:

AF XY:

0.743

AC XY:

524967

AN XY:

706140

show subpopulations

African (AFR)

AF:

0.668

AC:

22033

AN:

32978

American (AMR)

AF:

0.735

AC:

30201

AN:

41070

Ashkenazi Jewish (ASJ)

AF:

0.666

AC:

16868

AN:

25338

East Asian (EAS)

AF:

0.717

AC:

27700

AN:

38634

South Asian (SAS)

AF:

0.633

AC:

52620

AN:

83082

European-Finnish (FIN)

AF:

0.706

AC:

35070

AN:

49664

Middle Eastern (MID)

AF:

0.690

AC:

2972

AN:

4310

European-Non Finnish (NFE)

AF:

0.764

AC:

836707

AN:

1094546

Other (OTH)

AF:

0.730

AC:

42980

AN:

58858

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

14042

28084

42125

56167

70209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20282

40564

60846

81128

101410

<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:

0.725

AC:

110300

AN:

152162

Hom.:

40220

Cov.:

AF XY:

0.721

AC XY:

53653

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.671

AC:

27841

AN:

41508

American (AMR)

AF:

0.744

AC:

11381

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

2323

AN:

3470

East Asian (EAS)

AF:

0.734

AC:

3796

AN:

5172

South Asian (SAS)

AF:

0.620

AC:

2994

AN:

4826

European-Finnish (FIN)

AF:

0.709

AC:

7520

AN:

10604

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.766

AC:

52073

AN:

67962

Other (OTH)

AF:

0.712

AC:

1504

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1605

3210

4816

6421

8026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

838

1676

2514

3352

4190

<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:

0.690

Hom.:

4950

Bravo

AF:

0.726

Asia WGS

AF:

0.641

AC:

2231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.1

(source)

DANN

Benign

0.48

PhyloP100

-0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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