1-159439859-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012351.3(OR10J1):āc.68A>Gā(p.Gln23Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012351.3 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 |
---|---|---|---|---|---|---|---|---|
OR10J1 | NM_012351.3 | c.68A>G | p.Gln23Arg | missense_variant | 1/1 | ENST00000423932.6 | NP_036483.3 | |
OR10J1 | NM_001363557.2 | c.68A>G | p.Gln23Arg | missense_variant | 5/5 | NP_001350486.1 | ||
OR10J1 | NM_001363558.2 | c.68A>G | p.Gln23Arg | missense_variant | 4/4 | NP_001350487.1 | ||
OR10J1 | XM_047417793.1 | c.68A>G | p.Gln23Arg | missense_variant | 2/2 | XP_047273749.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR10J1 | ENST00000423932.6 | c.68A>G | p.Gln23Arg | missense_variant | 1/1 | 6 | NM_012351.3 | ENSP00000399078.4 | ||
ENSG00000228560 | ENST00000431862.1 | n.227+28983T>C | intron_variant | 1 | ||||||
OR10J1 | ENST00000641630.1 | c.101A>G | p.Gln34Arg | missense_variant | 1/1 | ENSP00000492902.1 | ||||
OR10J1 | ENST00000642080.1 | c.68A>G | p.Gln23Arg | missense_variant | 2/2 | ENSP00000493228.1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251364Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135844
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461864Hom.: 0 Cov.: 48 AF XY: 0.00000550 AC XY: 4AN XY: 727232
GnomAD4 genome AF: 0.000144 AC: 22AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.101A>G (p.Q34R) alteration is located in exon 1 (coding exon 1) of the OR10J1 gene. This alteration results from a A to G substitution at nucleotide position 101, causing the glutamine (Q) at amino acid position 34 to be replaced by an arginine (R). 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