11-56232560-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001004746.4(OR5T2):c.503G>A(p.Gly168Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000954 in 1,613,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004746.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
OR5T2 | ENST00000641661.1 | c.503G>A | p.Gly168Glu | missense_variant | Exon 2 of 2 | NM_001004746.4 | ENSP00000493233.1 |
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 250974Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135636
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461602Hom.: 0 Cov.: 33 AF XY: 0.0000921 AC XY: 67AN XY: 727100
GnomAD4 genome AF: 0.0000987 AC: 15AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.626G>A (p.G209E) alteration is located in exon 1 (coding exon 1) of the OR5T2 gene. This alteration results from a G to A substitution at nucleotide position 626, causing the glycine (G) at amino acid position 209 to be replaced by a glutamic acid (E). 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