NM_004416.3:c.460A>T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004416.3(DTX1):c.460A>T(p.Asn154Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004416.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DTX1 | NM_004416.3 | c.460A>T | p.Asn154Tyr | missense_variant | Exon 3 of 10 | ENST00000548759.2 | NP_004407.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151798Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 34
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151798Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74118
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.460A>T (p.N154Y) alteration is located in exon 2 (coding exon 2) of the DTX1 gene. This alteration results from a A to T substitution at nucleotide position 460, causing the asparagine (N) at amino acid position 154 to be replaced by a tyrosine (Y). 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