chr11-58118993-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005211.2(OR9I1):c.452G>A(p.Cys151Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 1,613,818 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005211.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR9I1 | NM_001005211.2 | c.452G>A | p.Cys151Tyr | missense_variant | 3/3 | ENST00000641439.1 | |
OR9Q1 | NM_001005212.4 | c.-14-60438C>T | intron_variant | ENST00000335397.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR9I1 | ENST00000641439.1 | c.452G>A | p.Cys151Tyr | missense_variant | 3/3 | NM_001005211.2 | P1 | ||
OR9Q1 | ENST00000335397.3 | c.-14-60438C>T | intron_variant | NM_001005212.4 | P1 | ||||
OR9I1 | ENST00000641478.1 | c.452G>A | p.Cys151Tyr | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152184Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000759 AC: 19AN: 250372Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135332
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461634Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727122
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152184Hom.: 1 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.452G>A (p.C151Y) alteration is located in exon 1 (coding exon 1) of the OR9I1 gene. This alteration results from a G to A substitution at nucleotide position 452, causing the cysteine (C) at amino acid position 151 to be replaced by a tyrosine (Y). 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