rs28757581
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001005216.4(OR2J3):āc.337A>Gā(p.Thr113Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,613,856 control chromosomes in the GnomAD database, including 15,213 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Affects (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001005216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2J3 | NM_001005216.4 | c.337A>G | p.Thr113Ala | missense_variant | 4/4 | ENST00000641151.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2J3 | ENST00000641151.2 | c.337A>G | p.Thr113Ala | missense_variant | 4/4 | NM_001005216.4 | P1 | ||
OR2J3 | ENST00000377169.2 | c.337A>G | p.Thr113Ala | missense_variant | 1/1 | P1 | |||
OR2J3 | ENST00000641960.1 | c.337A>G | p.Thr113Ala | missense_variant | 5/5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.179 AC: 27203AN: 151992Hom.: 3258 Cov.: 32
GnomAD3 exomes AF: 0.142 AC: 35484AN: 249358Hom.: 3088 AF XY: 0.138 AC XY: 18647AN XY: 135316
GnomAD4 exome AF: 0.119 AC: 174437AN: 1461746Hom.: 11947 Cov.: 34 AF XY: 0.120 AC XY: 87069AN XY: 727198
GnomAD4 genome ? AF: 0.179 AC: 27253AN: 152110Hom.: 3266 Cov.: 32 AF XY: 0.178 AC XY: 13205AN XY: 74388
ClinVar
Submissions by phenotype
C3HEX, ability to smell Other:1
Affects, no assertion criteria provided | literature only | OMIM | Sep 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at