NM_198571.3:c.749G>C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198571.3(NAT16):āc.749G>Cā(p.Arg250Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000563 in 1,597,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R250Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_198571.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAT16 | NM_198571.3 | c.749G>C | p.Arg250Pro | missense_variant | Exon 4 of 4 | ENST00000300303.7 | NP_940973.2 | |
NAT16 | NM_001369694.1 | c.749G>C | p.Arg250Pro | missense_variant | Exon 5 of 5 | NP_001356623.1 | ||
NAT16 | NM_001369695.1 | c.749G>C | p.Arg250Pro | missense_variant | Exon 4 of 4 | NP_001356624.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000922 AC: 2AN: 216850Hom.: 0 AF XY: 0.00000835 AC XY: 1AN XY: 119782
GnomAD4 exome AF: 0.00000484 AC: 7AN: 1445268Hom.: 0 Cov.: 33 AF XY: 0.00000417 AC XY: 3AN XY: 718680
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74464
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at