8-106684358-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001198533.2(OXR1):c.524C>T(p.Thr175Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000618 in 1,439,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001198533.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OXR1 | NM_001198533.2 | c.524C>T | p.Thr175Ile | missense_variant, splice_region_variant | 6/17 | ENST00000517566.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXR1 | ENST00000517566.7 | c.524C>T | p.Thr175Ile | missense_variant, splice_region_variant | 6/17 | 1 | NM_001198533.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000759 AC: 19AN: 250414Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135338
GnomAD4 exome AF: 0.0000303 AC: 39AN: 1287674Hom.: 0 Cov.: 20 AF XY: 0.0000277 AC XY: 18AN XY: 649772
GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74458
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2022 | The c.527C>T (p.T176I) alteration is located in exon 5 (coding exon 5) of the OXR1 gene. This alteration results from a C to T substitution at nucleotide position 527, causing the threonine (T) at amino acid position 176 to be replaced by an isoleucine (I). The p.T176I alteration is predicted to be tolerated by in silico analysis. 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