Variant rs35975875 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_145201.6(NAPRT):c.994C>T(p.Arg332Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00542 in 1,610,904 control chromosomes in the GnomAD database, including 44 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 0.0042 ( 5 hom., cov: 30)

Exomes 𝑓: 0.0055 ( 39 hom. )

Consequence

NAPRT
NM_145201.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.05

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.052319944).

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAPRT	NM_145201.6 link	c.994C>T	p.Arg332Cys	missense_variant	7/13	ENST00000449291.7	NP_660202.3	Q6XQN6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAPRT	ENST00000449291.7 link	c.994C>T	p.Arg332Cys	missense_variant	7/13	1	NM_145201.6	ENSP00000401508.2		Q6XQN6-1

Frequencies

GnomAD3 genomes

AF:

0.00423

AC:

643

AN:

152028

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00114

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00332

Gnomad FIN

AF:

0.00481

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.00597

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00464

AC:

1153

AN:

248268

Hom.:

AF XY:

0.00490

AC XY:

660

AN XY:

134652

show subpopulations

Gnomad AFR exome

AF:

0.000748

Gnomad AMR exome

AF:

0.000934

Gnomad ASJ exome

AF:

0.00555

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00489

Gnomad FIN exome

AF:

0.00649

Gnomad NFE exome

AF:

0.00657

Gnomad OTH exome

AF:

0.00529

GnomAD4 exome

AF:

0.00554

AC:

8083

AN:

1458756

Hom.:

Cov.:

AF XY:

0.00570

AC XY:

4135

AN XY:

725460

show subpopulations

Gnomad4 AFR exome

AF:

0.000718

Gnomad4 AMR exome

AF:

0.00130

Gnomad4 ASJ exome

AF:

0.00461

Gnomad4 EAS exome

AF:

0.0000757

Gnomad4 SAS exome

AF:

0.00465

Gnomad4 FIN exome

AF:

0.00797

Gnomad4 NFE exome

AF:

0.00608

Gnomad4 OTH exome

AF:

0.00481

GnomAD4 genome

AF:

0.00422

AC:

642

AN:

152148

Hom.:

Cov.:

AF XY:

0.00401

AC XY:

298

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00353

Gnomad4 FIN

AF:

0.00481

Gnomad4 NFE

AF:

0.00597

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00591

Hom.:

Bravo

AF:

0.00378

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.00389

AC:

ESP6500AA

AF:

0.000909

AC:

ESP6500EA

AF:

0.00628

AC:

ExAC

AF:

0.00494

AC:

599

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.00485

EpiControl

AF:

0.00546

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.10

BayesDel_noAF

Uncertain

0.080

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.50

D;D;.

Eigen

Pathogenic

0.74

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.94

D;.;.

M_CAP

Uncertain

0.27

MetaRNN

Benign

0.052

T;T;T

MetaSVM

Uncertain

0.071

MutationAssessor

Pathogenic

4.2

.;H;H

PrimateAI

Benign

0.45

PROVEAN

Pathogenic

-7.2

D;D;D

REVEL

Uncertain

0.54

Sift

Pathogenic

0.0

D;D;D

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

1.0

D;D;D

Vest4

0.80

MVP

0.64

MPC

0.43

ClinPred

0.26

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.74

gMVP

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over