rs41496055
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005746.3(NAMPT):c.970-92G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,356,792 control chromosomes in the GnomAD database, including 443 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 0.013 ( 140 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 303 hom. )
Consequence
NAMPT
NM_005746.3 intron
NM_005746.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.346
Genes affected
NAMPT (HGNC:30092): (nicotinamide phosphoribosyltransferase) This gene encodes a protein that catalyzes the condensation of nicotinamide with 5-phosphoribosyl-1-pyrophosphate to yield nicotinamide mononucleotide, one step in the biosynthesis of nicotinamide adenine dinucleotide. The protein belongs to the nicotinic acid phosphoribosyltransferase (NAPRTase) family and is thought to be involved in many important biological processes, including metabolism, stress response and aging. This gene has a pseudogene on chromosome 10. [provided by RefSeq, Feb 2011]
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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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAMPT | NM_005746.3 | c.970-92G>T | intron_variant | ENST00000222553.8 | |||
NAMPT | XM_047419699.1 | c.970-92G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAMPT | ENST00000222553.8 | c.970-92G>T | intron_variant | 1 | NM_005746.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0126 AC: 1915AN: 151880Hom.: 142 Cov.: 32
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GnomAD4 exome AF: 0.00383 AC: 4616AN: 1204794Hom.: 303 AF XY: 0.00324 AC XY: 1967AN XY: 607880
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GnomAD4 genome AF: 0.0126 AC: 1913AN: 151998Hom.: 140 Cov.: 32 AF XY: 0.0152 AC XY: 1131AN XY: 74294
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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