6-29112263-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001005216.4(OR2J3):c.373C>T(p.Arg125Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR2J3 | NM_001005216.4 | c.373C>T | p.Arg125Cys | missense_variant | Exon 4 of 4 | ENST00000641151.2 | NP_001005216.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR2J3 | ENST00000641151.2 | c.373C>T | p.Arg125Cys | missense_variant | Exon 4 of 4 | NM_001005216.4 | ENSP00000492961.1 | |||
OR2J3 | ENST00000377169.2 | c.373C>T | p.Arg125Cys | missense_variant | Exon 1 of 1 | 6 | ENSP00000366374.1 | |||
OR2J3 | ENST00000641960.1 | c.373C>T | p.Arg125Cys | missense_variant | Exon 5 of 5 | ENSP00000493439.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249296Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135270
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.373C>T (p.R125C) alteration is located in exon 1 (coding exon 1) of the OR2J3 gene. This alteration results from a C to T substitution at nucleotide position 373, causing the arginine (R) at amino acid position 125 to be replaced by a cysteine (C). 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