rs17126356
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000662.8(NAT1):c.-6-272T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00832 in 319,368 control chromosomes in the GnomAD database, including 65 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 0.015 ( 60 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 5 hom. )
Consequence
NAT1
NM_000662.8 intron
NM_000662.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.464
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0149 (2268/152290) while in subpopulation AFR AF= 0.0507 (2107/41560). AF 95% confidence interval is 0.0489. There are 60 homozygotes in gnomad4. There are 1056 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 2268 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT1 | NM_000662.8 | c.-6-272T>A | intron_variant | ENST00000307719.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT1 | ENST00000307719.9 | c.-6-272T>A | intron_variant | 1 | NM_000662.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0149 AC: 2262AN: 152172Hom.: 58 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.00232 AC: 388AN: 167078Hom.: 5 Cov.: 3 AF XY: 0.00213 AC XY: 184AN XY: 86442
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GnomAD4 genome ? AF: 0.0149 AC: 2268AN: 152290Hom.: 60 Cov.: 32 AF XY: 0.0142 AC XY: 1056AN XY: 74468
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at