8-106519025-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001198533.2(OXR1):c.106G>A(p.Ala36Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000286 in 1,399,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001198533.2 missense
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.106G>A | p.Ala36Thr | missense_variant | 3/17 | ENST00000517566.7 | |
OXR1-AS1 | XR_007061059.1 | n.3261C>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXR1 | ENST00000517566.7 | c.106G>A | p.Ala36Thr | missense_variant | 3/17 | 1 | NM_001198533.2 | P3 | |
OXR1 | ENST00000442977.6 | c.109G>A | p.Ala37Thr | missense_variant | 2/16 | 2 | A2 | ||
OXR1 | ENST00000531443.6 | c.106G>A | p.Ala36Thr | missense_variant | 3/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1399640Hom.: 0 Cov.: 31 AF XY: 0.00000290 AC XY: 2AN XY: 690330
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.109G>A (p.A37T) alteration is located in exon 2 (coding exon 2) of the OXR1 gene. This alteration results from a G to A substitution at nucleotide position 109, causing the alanine (A) at amino acid position 37 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
Publications
No publications associated with this variant yet.