rs4987076
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000662.8(NAT1):c.445G>A(p.Val149Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 1,614,078 control chromosomes in the GnomAD database, including 483 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000662.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT1 | NM_000662.8 | c.445G>A | p.Val149Ile | missense_variant | 3/3 | ENST00000307719.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT1 | ENST00000307719.9 | c.445G>A | p.Val149Ile | missense_variant | 3/3 | 1 | NM_000662.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0181 AC: 2751AN: 152122Hom.: 49 Cov.: 32
GnomAD3 exomes AF: 0.0203 AC: 5103AN: 251186Hom.: 80 AF XY: 0.0217 AC XY: 2941AN XY: 135736
GnomAD4 exome AF: 0.0218 AC: 31878AN: 1461838Hom.: 434 Cov.: 32 AF XY: 0.0224 AC XY: 16269AN XY: 727232
GnomAD4 genome ? AF: 0.0181 AC: 2759AN: 152240Hom.: 49 Cov.: 32 AF XY: 0.0174 AC XY: 1293AN XY: 74424
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
NAT1*17 ALLELE Other:1
other, no assertion criteria provided | literature only | OMIM | Apr 20, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at