rs896954
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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
NM_145201.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.284
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]
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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 | UniProt |
---|---|---|---|---|---|---|---|
NAPRT | NM_145201.6 | c.294C>T | p.Ala98= | synonymous_variant | 2/13 | ENST00000449291.7 | |
NAPRT | NM_001286829.2 | c.294C>T | p.Ala98= | synonymous_variant | 2/13 | ||
NAPRT | NM_001363145.1 | c.294C>T | p.Ala98= | synonymous_variant | 2/12 | ||
NAPRT | NM_001363146.1 | c.-275C>T | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAPRT | ENST00000449291.7 | c.294C>T | p.Ala98= | synonymous_variant | 2/13 | 1 | NM_145201.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.154 AC: 23414AN: 152056Hom.: 2001 Cov.: 33
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GnomAD3 exomes AF: 0.182 AC: 44532AN: 244450Hom.: 4383 AF XY: 0.184 AC XY: 24637AN XY: 133540
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GnomAD4 exome AF: 0.173 AC: 252170AN: 1459772Hom.: 22847 Cov.: 39 AF XY: 0.175 AC XY: 127133AN XY: 726140
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GnomAD4 genome ? AF: 0.154 AC: 23414AN: 152174Hom.: 2001 Cov.: 33 AF XY: 0.157 AC XY: 11706AN XY: 74396
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Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at