chr7-101172440-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198571.3(NAT16):c.749G>A(p.Arg250Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000282 in 1,597,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 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>A | p.Arg250Gln | missense_variant | Exon 4 of 4 | ENST00000300303.7 | NP_940973.2 | |
NAT16 | NM_001369694.1 | c.749G>A | p.Arg250Gln | missense_variant | Exon 5 of 5 | NP_001356623.1 | ||
NAT16 | NM_001369695.1 | c.749G>A | p.Arg250Gln | missense_variant | Exon 4 of 4 | NP_001356624.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 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: 0.0000284 AC: 41AN: 1445268Hom.: 0 Cov.: 33 AF XY: 0.0000292 AC XY: 21AN XY: 718680
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.749G>A (p.R250Q) alteration is located in exon 4 (coding exon 3) of the NAT16 gene. This alteration results from a G to A substitution at nucleotide position 749, causing the arginine (R) at amino acid position 250 to be replaced by a glutamine (Q). 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