chr8-18400193-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000015.3(NAT2):c.190C>T(p.Arg64Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,612,994 control chromosomes in the GnomAD database, including 2 homozygotes. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R64Q) has been classified as Likely benign.
Frequency
Consequence
NM_000015.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT2 | NM_000015.3 | c.190C>T | p.Arg64Trp | missense_variant | 2/2 | ENST00000286479.4 | |
NAT2 | XM_017012938.2 | c.190C>T | p.Arg64Trp | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT2 | ENST00000286479.4 | c.190C>T | p.Arg64Trp | missense_variant | 2/2 | 1 | NM_000015.3 | P1 | |
NAT2 | ENST00000520116.1 | c.-57-144C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 152024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000267 AC: 67AN: 250634Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135460
GnomAD4 exome AF: 0.000115 AC: 168AN: 1460970Hom.: 2 Cov.: 30 AF XY: 0.000118 AC XY: 86AN XY: 726664
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74232
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at