rs28359482
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001291962.2(NAT1):c.-18+90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 152,254 control chromosomes in the GnomAD database, including 1 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 0.0025 ( 1 hom., cov: 32)
Exomes 𝑓: 0.013 ( 0 hom. )
Consequence
NAT1
NM_001291962.2 intron
NM_001291962.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.30
Genes affected
NAT1 (HGNC:7645): (N-acetyltransferase 1) This gene is one of two arylamine N-acetyltransferase (NAT) genes in the human genome, and is orthologous to the mouse and rat Nat2 genes. The enzyme encoded by this gene catalyzes the transfer of an acetyl group from acetyl-CoA to various arylamine and hydrazine substrates. This enzyme helps metabolize drugs and other xenobiotics, and functions in folate catabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
High AC in GnomAd4 at 379 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAT1 | NM_001291962.2 | c.-18+90T>C | intron_variant | NP_001278891.1 | ||||
NAT1 | NM_001160179.3 | c.-86+90T>C | intron_variant | NP_001153651.1 | ||||
NAT1 | XM_047422397.1 | c.-640-47T>C | intron_variant | XP_047278353.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAT1 | ENST00000517441.5 | n.267+90T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00249 AC: 378AN: 152058Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.0128 AC: 1AN: 78Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 60
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GnomAD4 genome AF: 0.00249 AC: 379AN: 152176Hom.: 1 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74424
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at