rs4986991
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_000662.8(NAT1):āc.777T>Cā(p.Ser259=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000868 in 1,607,426 control chromosomes in the GnomAD database, including 8 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 0.0041 ( 4 hom., cov: 32)
Exomes š: 0.00053 ( 4 hom. )
Consequence
NAT1
NM_000662.8 synonymous
NM_000662.8 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.33
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=-0.91).
BP7
?
Synonymous conserved (PhyloP=-1.33 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000528 (768/1455190) while in subpopulation AFR AF= 0.0166 (551/33224). AF 95% confidence interval is 0.0154. There are 4 homozygotes in gnomad4_exome. There are 345 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 628 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT1 | NM_000662.8 | c.777T>C | p.Ser259= | synonymous_variant | 3/3 | ENST00000307719.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT1 | ENST00000307719.9 | c.777T>C | p.Ser259= | synonymous_variant | 3/3 | 1 | NM_000662.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00411 AC: 625AN: 152118Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00126 AC: 308AN: 244954Hom.: 2 AF XY: 0.000943 AC XY: 125AN XY: 132520
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GnomAD4 exome AF: 0.000528 AC: 768AN: 1455190Hom.: 4 Cov.: 31 AF XY: 0.000477 AC XY: 345AN XY: 723318
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GnomAD4 genome ? AF: 0.00413 AC: 628AN: 152236Hom.: 4 Cov.: 32 AF XY: 0.00427 AC XY: 318AN XY: 74430
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ClinVar
Not reported inComputational scores
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Name
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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