rs2305496
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145201.6(NAPRT):c.354+37G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,574,126 control chromosomes in the GnomAD database, including 14,995 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 0.16 ( 2435 hom., cov: 33)
Exomes 𝑓: 0.12 ( 12560 hom. )
Consequence
NAPRT
NM_145201.6 intron
NM_145201.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.687
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAPRT | NM_145201.6 | c.354+37G>T | intron_variant | ENST00000449291.7 | |||
NAPRT | NM_001286829.2 | c.354+37G>T | intron_variant | ||||
NAPRT | NM_001363145.1 | c.354+37G>T | intron_variant | ||||
NAPRT | NM_001363146.1 | c.-215+37G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAPRT | ENST00000449291.7 | c.354+37G>T | intron_variant | 1 | NM_145201.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24410AN: 152016Hom.: 2438 Cov.: 33
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GnomAD3 exomes AF: 0.169 AC: 29821AN: 176260Hom.: 3335 AF XY: 0.162 AC XY: 15802AN XY: 97346
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GnomAD4 exome AF: 0.118 AC: 167850AN: 1421992Hom.: 12560 Cov.: 35 AF XY: 0.119 AC XY: 83992AN XY: 704668
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GnomAD4 genome ? AF: 0.161 AC: 24423AN: 152134Hom.: 2435 Cov.: 33 AF XY: 0.161 AC XY: 11992AN XY: 74386
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at