rs744650
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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.894C>T(p.Pro298=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.024 in 1,610,952 control chromosomes in the GnomAD database, including 596 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 0.021 ( 57 hom., cov: 33)
Exomes 𝑓: 0.024 ( 539 hom. )
Consequence
NAPRT
NM_145201.6 synonymous
NM_145201.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0300
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=-0.52).
BP7
?
Synonymous conserved (PhyloP=0.03 with no splicing effect.
BA1
?
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0506 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAPRT | NM_145201.6 | c.894C>T | p.Pro298= | synonymous_variant | 7/13 | ENST00000449291.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAPRT | ENST00000449291.7 | c.894C>T | p.Pro298= | synonymous_variant | 7/13 | 1 | NM_145201.6 | P1 | |
ENST00000531730.1 | n.437-101G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0211 AC: 3211AN: 152050Hom.: 57 Cov.: 33
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GnomAD3 exomes AF: 0.0253 AC: 6234AN: 246460Hom.: 120 AF XY: 0.0258 AC XY: 3451AN XY: 133922
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GnomAD4 exome AF: 0.0243 AC: 35413AN: 1458784Hom.: 539 Cov.: 36 AF XY: 0.0245 AC XY: 17748AN XY: 725612
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GnomAD4 genome ? AF: 0.0211 AC: 3208AN: 152168Hom.: 57 Cov.: 33 AF XY: 0.0233 AC XY: 1735AN XY: 74400
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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