9-122568110-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001004454.2(OR1L8):c.368G>A(p.Arg123His) variant causes a missense change. The variant allele was found at a frequency of 0.0000644 in 1,613,706 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).
Frequency
Consequence
NM_001004454.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1L8 | NM_001004454.2 | c.368G>A | p.Arg123His | missense_variant | Exon 5 of 5 | ENST00000641027.1 | NP_001004454.1 | |
OR1L8 | XM_017014285.2 | c.368G>A | p.Arg123His | missense_variant | Exon 3 of 4 | XP_016869774.1 | ||
OR1L8 | XM_017014286.2 | c.368G>A | p.Arg123His | missense_variant | Exon 2 of 2 | XP_016869775.1 | ||
OR1J2 | XR_007061271.1 | n.1541-11843C>T | intron_variant | Intron 4 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250596Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135394
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461574Hom.: 2 Cov.: 36 AF XY: 0.0000756 AC XY: 55AN XY: 727058
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.368G>A (p.R123H) alteration is located in exon 1 (coding exon 1) of the OR1L8 gene. This alteration results from a G to A substitution at nucleotide position 368, causing the arginine (R) at amino acid position 123 to be replaced by a histidine (H). 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