Variant rs896954 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_145201.6(NAPRT):c.294C>T(p.Ala98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,611,946 control chromosomes in the GnomAD database, including 24,848 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 0.15 ( 2001 hom., cov: 33)

Exomes 𝑓: 0.17 ( 22847 hom. )

Consequence

NAPRT
NM_145201.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.284

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-0.284 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NAPRT	NM_145201.6 linkuse as main transcript	c.294C>T	p.Ala98=	synonymous_variant	2/13	ENST00000449291.7	NP_660202.3
NAPRT	NM_001286829.2 linkuse as main transcript	c.294C>T	p.Ala98=	synonymous_variant	2/13		NP_001273758.1
NAPRT	NM_001363145.1 linkuse as main transcript	c.294C>T	p.Ala98=	synonymous_variant	2/12		NP_001350074.1
NAPRT	NM_001363146.1 linkuse as main transcript	c.-275C>T		5_prime_UTR_variant	2/12		NP_001350075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAPRT	ENST00000449291.7 linkuse as main transcript	c.294C>T	p.Ala98=	synonymous_variant	2/13	1	NM_145201.6	ENSP00000401508	P1	Q6XQN6-1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23414

AN:

152056

Hom.:

2001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0943

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.172

GnomAD3 exomes

AF:

0.182

AC:

44532

AN:

244450

Hom.:

4383

AF XY:

0.184

AC XY:

24637

AN XY:

133540

show subpopulations

Gnomad AFR exome

AF:

0.0935

Gnomad AMR exome

AF:

0.214

Gnomad ASJ exome

AF:

0.258

Gnomad EAS exome

AF:

0.111

Gnomad SAS exome

AF:

0.231

Gnomad FIN exome

AF:

0.217

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.193

GnomAD4 exome

AF:

0.173

AC:

252170

AN:

1459772

Hom.:

22847

Cov.:

AF XY:

0.175

AC XY:

127133

AN XY:

726140

show subpopulations

Gnomad4 AFR exome

AF:

0.0959

Gnomad4 AMR exome

AF:

0.213

Gnomad4 ASJ exome

AF:

0.258

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.230

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.165

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.154

AC:

23414

AN:

152174

Hom.:

2001

Cov.:

AF XY:

0.157

AC XY:

11706

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0940

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.221

Gnomad4 NFE

AF:

0.165

Gnomad4 OTH

AF:

0.171

Alfa

AF:

0.163

Hom.:

2021

Bravo

AF:

0.149

Asia WGS

AF:

0.181

AC:

626

AN:

3476

EpiCase

AF:

0.166

EpiControl

AF:

0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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