Variant rs2290416 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.1284C>T(p.Gly428=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 1,591,434 control chromosomes in the GnomAD database, including 6,816 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 0.077 ( 523 hom., cov: 32)

Exomes 𝑓: 0.090 ( 6293 hom. )

Consequence

NAPRT
NM_145201.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.338

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:

(HGNC:):

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=-0.78).

BP7

Synonymous conserved (PhyloP=-0.338 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAPRT	NM_145201.6 linkuse as main transcript	c.1284C>T	p.Gly428=	synonymous_variant	10/13	ENST00000449291.7	NP_660202.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAPRT	ENST00000449291.7 linkuse as main transcript	c.1284C>T	p.Gly428=	synonymous_variant	10/13	1	NM_145201.6	ENSP00000401508	P1	Q6XQN6-1
	ENST00000531730.1 linkuse as main transcript	n.436+324G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0768

AC:

11685

AN:

152064

Hom.:

523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0387

Gnomad AMI

AF:

0.0505

Gnomad AMR

AF:

0.0785

Gnomad ASJ

AF:

0.0919

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.0769

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0874

Gnomad OTH

AF:

0.0895

GnomAD3 exomes

AF:

0.0922

AC:

22977

AN:

249258

Hom.:

1237

AF XY:

0.0981

AC XY:

13249

AN XY:

135002

show subpopulations

Gnomad AFR exome

AF:

0.0336

Gnomad AMR exome

AF:

0.0529

Gnomad ASJ exome

AF:

0.0979

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.151

Gnomad FIN exome

AF:

0.0790

Gnomad NFE exome

AF:

0.0892

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.0898

AC:

129268

AN:

1439252

Hom.:

6293

Cov.:

AF XY:

0.0923

AC XY:

65590

AN XY:

710690

show subpopulations

Gnomad4 AFR exome

AF:

0.0384

Gnomad4 AMR exome

AF:

0.0565

Gnomad4 ASJ exome

AF:

0.0959

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.0755

Gnomad4 NFE exome

AF:

0.0864

Gnomad4 OTH exome

AF:

0.0943

GnomAD4 genome

AF:

0.0768

AC:

11690

AN:

152182

Hom.:

523

Cov.:

AF XY:

0.0784

AC XY:

5837

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0387

Gnomad4 AMR

AF:

0.0785

Gnomad4 ASJ

AF:

0.0919

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.0769

Gnomad4 NFE

AF:

0.0874

Gnomad4 OTH

AF:

0.0895

Alfa

AF:

0.0901

Hom.:

1219

Bravo

AF:

0.0731

Asia WGS

AF:

0.171

AC:

595

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.9

DANN

Benign

0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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