1-248453501-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 3P and 8B. PM2PP2BP4_StrongBS2
The NM_001004136.2(OR2T2):c.704G>A(p.Arg235Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000283 in 1,587,330 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004136.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2T2 | NM_001004136.2 | c.704G>A | p.Arg235Gln | missense_variant | 4/4 | ENST00000641925.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2T2 | ENST00000641925.2 | c.704G>A | p.Arg235Gln | missense_variant | 4/4 | NM_001004136.2 | P1 | ||
OR2T2 | ENST00000642130.1 | c.704G>A | p.Arg235Gln | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000121 AC: 18AN: 148372Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000704 AC: 17AN: 241540Hom.: 2 AF XY: 0.0000536 AC XY: 7AN XY: 130496
GnomAD4 exome AF: 0.0000188 AC: 27AN: 1438958Hom.: 1 Cov.: 35 AF XY: 0.0000223 AC XY: 16AN XY: 715902
GnomAD4 genome ? AF: 0.000121 AC: 18AN: 148372Hom.: 0 Cov.: 27 AF XY: 0.000111 AC XY: 8AN XY: 72198
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.704G>A (p.R235Q) alteration is located in exon 1 (coding exon 1) of the OR2T2 gene. This alteration results from a G to A substitution at nucleotide position 704, causing the arginine (R) at amino acid position 235 to be replaced by a glutamine (Q). 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