16-1979144-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_172167.3(NOXO1):c.1024G>A(p.Val342Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000177 in 1,466,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_172167.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOXO1 | ENST00000356120.9 | c.1024G>A | p.Val342Ile | missense_variant | Exon 8 of 8 | 1 | NM_172167.3 | ENSP00000348435.4 | ||
TBL3 | ENST00000568546.6 | c.*459C>T | 3_prime_UTR_variant | Exon 22 of 22 | 1 | NM_006453.3 | ENSP00000454836.1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 151986Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000666 AC: 5AN: 75114Hom.: 0 AF XY: 0.0000927 AC XY: 4AN XY: 43144
GnomAD4 exome AF: 0.0000122 AC: 16AN: 1314972Hom.: 0 Cov.: 34 AF XY: 0.0000139 AC XY: 9AN XY: 645830
GnomAD4 genome AF: 0.0000658 AC: 10AN: 151986Hom.: 0 Cov.: 34 AF XY: 0.0000673 AC XY: 5AN XY: 74242
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at