rs4986992
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The ENST00000307719.9(NAT1):āc.21T>Gā(p.Leu7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000937 in 1,613,310 control chromosomes in the GnomAD database, including 9 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: š 0.0045 ( 5 hom., cov: 32)
Exomes š: 0.00056 ( 4 hom. )
Consequence
NAT1
ENST00000307719.9 synonymous
ENST00000307719.9 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.152
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP7
Synonymous conserved (PhyloP=-0.152 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000561 (820/1460994) while in subpopulation AFR AF= 0.0178 (594/33460). AF 95% confidence interval is 0.0166. There are 4 homozygotes in gnomad4_exome. There are 365 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 691 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAT1 | NM_000662.8 | c.21T>G | p.Leu7= | synonymous_variant | 3/3 | ENST00000307719.9 | NP_000653.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAT1 | ENST00000307719.9 | c.21T>G | p.Leu7= | synonymous_variant | 3/3 | 1 | NM_000662.8 | ENSP00000307218 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00451 AC: 686AN: 152198Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00137 AC: 344AN: 250498Hom.: 2 AF XY: 0.000997 AC XY: 135AN XY: 135362
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GnomAD4 exome AF: 0.000561 AC: 820AN: 1460994Hom.: 4 Cov.: 31 AF XY: 0.000502 AC XY: 365AN XY: 726672
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GnomAD4 genome AF: 0.00454 AC: 691AN: 152316Hom.: 5 Cov.: 32 AF XY: 0.00467 AC XY: 348AN XY: 74478
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at