rs4986997
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_000015.3(NAT2):āc.411A>Cā(p.Leu137Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,611,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000015.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT2 | NM_000015.3 | c.411A>C | p.Leu137Phe | missense_variant | 2/2 | ENST00000286479.4 | |
NAT2 | XM_017012938.2 | c.411A>C | p.Leu137Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT2 | ENST00000286479.4 | c.411A>C | p.Leu137Phe | missense_variant | 2/2 | 1 | NM_000015.3 | P1 | |
NAT2 | ENST00000520116.1 | c.21A>C | p.Leu7Phe | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151964Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248606Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134346
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459986Hom.: 0 Cov.: 58 AF XY: 0.00000551 AC XY: 4AN XY: 726262
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151964Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74210
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at