rs59744560
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000609281.2(NAMPT-AS1):n.633C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0947 in 152,516 control chromosomes in the GnomAD database, including 930 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 0.095 ( 926 hom., cov: 32)
Exomes 𝑓: 0.16 ( 4 hom. )
Consequence
NAMPT-AS1
ENST00000609281.2 non_coding_transcript_exon
ENST00000609281.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.542
Genes affected
NAMPT-AS1 (HGNC:56696): (NAMPT antisense RNA 1)
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=-0.57).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAMPT | XM_047419699.1 | c.-389G>T | 5_prime_UTR_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAMPT-AS1 | ENST00000609281.2 | n.633C>A | non_coding_transcript_exon_variant | 1/1 | |||||
NAMPT | ENST00000424768.2 | c.-389G>T | 5_prime_UTR_variant | 1/12 | 4 | P4 | |||
NAMPT | ENST00000681255.1 | c.-339G>T | 5_prime_UTR_variant | 1/12 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0946 AC: 14389AN: 152024Hom.: 926 Cov.: 32
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GnomAD4 exome AF: 0.155 AC: 58AN: 374Hom.: 4 Cov.: 0 AF XY: 0.172 AC XY: 34AN XY: 198
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GnomAD4 genome AF: 0.0945 AC: 14383AN: 152142Hom.: 926 Cov.: 32 AF XY: 0.0917 AC XY: 6820AN XY: 74366
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at