9-122477433-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001004451.1(OR1J1):āc.494A>Gā(p.Gln165Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000514 in 1,613,824 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 Likely benign (ā ).
Frequency
Consequence
NM_001004451.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1J1 | NM_001004451.1 | c.494A>G | p.Gln165Arg | missense_variant | 1/1 | ENST00000259357.3 | NP_001004451.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR1J1 | ENST00000259357.3 | c.494A>G | p.Gln165Arg | missense_variant | 1/1 | 6 | NM_001004451.1 | ENSP00000259357.2 | ||
ENSG00000234156 | ENST00000431442.2 | n.1186+8248T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250564Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135392
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461708Hom.: 0 Cov.: 34 AF XY: 0.0000385 AC XY: 28AN XY: 727134
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74300
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at