16-1979164-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_172167.3(NOXO1):āc.1004T>Cā(p.Ile335Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000663 in 150,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_172167.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOXO1 | ENST00000356120.9 | c.1004T>C | p.Ile335Thr | missense_variant | Exon 8 of 8 | 1 | NM_172167.3 | ENSP00000348435.4 | ||
TBL3 | ENST00000568546.6 | c.*479A>G | 3_prime_UTR_variant | Exon 22 of 22 | 1 | NM_006453.3 | ENSP00000454836.1 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150660Hom.: 0 Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1277266Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 626674
GnomAD4 genome AF: 0.00000663 AC: 1AN: 150778Hom.: 0 Cov.: 34 AF XY: 0.0000136 AC XY: 1AN XY: 73680
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1019T>C (p.I340T) alteration is located in exon 8 (coding exon 8) of the NOXO1 gene. This alteration results from a T to C substitution at nucleotide position 1019, causing the isoleucine (I) at amino acid position 340 to be replaced by a threonine (T). 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