chr3-50297121-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001200016.2(NAA80):c.343G>A(p.Glu115Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000959 in 1,564,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign 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. E115G) has been classified as Likely benign.
Frequency
Consequence
NM_001200016.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA80 | NM_001200016.2 | c.343G>A | p.Glu115Lys | missense_variant | 2/2 | ENST00000443094.3 | |
HYAL3 | NM_003549.4 | c.-17-1502G>A | intron_variant | ENST00000336307.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA80 | ENST00000443094.3 | c.343G>A | p.Glu115Lys | missense_variant | 2/2 | 1 | NM_001200016.2 | A2 | |
HYAL3 | ENST00000336307.6 | c.-17-1502G>A | intron_variant | 1 | NM_003549.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000143 AC: 3AN: 209744Hom.: 0 AF XY: 0.0000176 AC XY: 2AN XY: 113480
GnomAD4 exome AF: 0.00000637 AC: 9AN: 1412162Hom.: 0 Cov.: 31 AF XY: 0.00000718 AC XY: 5AN XY: 696644
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.409G>A (p.E137K) alteration is located in exon 2 (coding exon 2) of the NAT6 gene. This alteration results from a G to A substitution at nucleotide position 409, causing the glutamic acid (E) at amino acid position 137 to be replaced by a lysine (K). 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