3-50296917-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_001200016.2(NAA80):c.547T>A(p.Tyr183Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,457,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y183C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001200016.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA80 | NM_001200016.2 | c.547T>A | p.Tyr183Asn | missense_variant | 2/2 | ENST00000443094.3 | |
HYAL3 | NM_003549.4 | c.-17-1298T>A | intron_variant | ENST00000336307.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA80 | ENST00000443094.3 | c.547T>A | p.Tyr183Asn | missense_variant | 2/2 | 1 | NM_001200016.2 | A2 | |
HYAL3 | ENST00000336307.6 | c.-17-1298T>A | intron_variant | 1 | NM_003549.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 237632Hom.: 0 AF XY: 0.00000766 AC XY: 1AN XY: 130508
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1457572Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725152
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.613T>A (p.Y205N) alteration is located in exon 2 (coding exon 2) of the NAT6 gene. This alteration results from a T to A substitution at nucleotide position 613, causing the tyrosine (Y) at amino acid position 205 to be replaced by an asparagine (N). 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