7-101173312-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198571.3(NAT16):c.521G>A(p.Arg174His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,814 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198571.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAT16 | NM_198571.3 | c.521G>A | p.Arg174His | missense_variant | Exon 3 of 4 | ENST00000300303.7 | NP_940973.2 | |
NAT16 | NM_001369694.1 | c.521G>A | p.Arg174His | missense_variant | Exon 4 of 5 | NP_001356623.1 | ||
NAT16 | NM_001369695.1 | c.521G>A | p.Arg174His | missense_variant | Exon 3 of 4 | NP_001356624.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAT16 | ENST00000300303.7 | c.521G>A | p.Arg174His | missense_variant | Exon 3 of 4 | 2 | NM_198571.3 | ENSP00000300303.2 | ||
NAT16 | ENST00000455377.5 | c.521G>A | p.Arg174His | missense_variant | Exon 4 of 5 | 1 | ENSP00000395125.1 | |||
NAT16 | ENST00000444446.1 | c.*52G>A | downstream_gene_variant | 4 | ENSP00000391769.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248920Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134804
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461654Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727136
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.521G>A (p.R174H) alteration is located in exon 3 (coding exon 2) of the NAT16 gene. This alteration results from a G to A substitution at nucleotide position 521, causing the arginine (R) at amino acid position 174 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at