rs200329286
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_172167.3(NOXO1):c.746A>T(p.Asp249Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,611,772 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 (★).
Frequency
Consequence
NM_172167.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOXO1 | ENST00000356120.9 | c.746A>T | p.Asp249Val | missense_variant | Exon 7 of 8 | 1 | NM_172167.3 | ENSP00000348435.4 | ||
TBL3 | ENST00000568546.6 | c.*812T>A | 3_prime_UTR_variant | Exon 22 of 22 | 1 | NM_006453.3 | ENSP00000454836.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152194Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000204 AC: 50AN: 245134Hom.: 0 AF XY: 0.000239 AC XY: 32AN XY: 133724
GnomAD4 exome AF: 0.000114 AC: 166AN: 1459578Hom.: 0 Cov.: 34 AF XY: 0.000123 AC XY: 89AN XY: 726030
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152194Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.761A>T (p.D254V) alteration is located in exon 7 (coding exon 7) of the NOXO1 gene. This alteration results from a A to T substitution at nucleotide position 761, causing the aspartic acid (D) at amino acid position 254 to be replaced by a valine (V). 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