9-122615236-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012364.1(OR1Q1):āc.499A>Cā(p.Ile167Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012364.1 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1Q1 | NM_012364.1 | c.499A>C | p.Ile167Leu | missense_variant | 1/1 | ENST00000297913.3 | NP_036496.1 | |
LOC124902265 | XR_007061759.1 | n.344+5186A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR1Q1 | ENST00000297913.3 | c.499A>C | p.Ile167Leu | missense_variant | 1/1 | 6 | NM_012364.1 | ENSP00000297913.2 | ||
ENSG00000234156 | ENST00000431442.2 | n.4767+5186A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461876Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.499A>C (p.I167L) alteration is located in exon 1 (coding exon 1) of the OR1Q1 gene. This alteration results from a A to C substitution at nucleotide position 499, causing the isoleucine (I) at amino acid position 167 to be replaced by a leucine (L). 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