chr1-158480641-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395749.1(OR10R2):c.731G>A(p.Arg244Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,613,792 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 Uncertain significance (★).
Frequency
Consequence
NM_001395749.1 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 | UniProt |
---|---|---|---|---|---|---|---|
OR10R2 | NM_001395749.1 | c.731G>A | p.Arg244Gln | missense_variant | 2/2 | ENST00000641067.1 | |
LOC107985213 | XR_001738258.2 | n.386-5974C>T | intron_variant, non_coding_transcript_variant | ||||
OR10R2 | NM_001004472.1 | c.764G>A | p.Arg255Gln | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR10R2 | ENST00000641067.1 | c.731G>A | p.Arg244Gln | missense_variant | 2/2 | NM_001395749.1 | P4 | ||
ENST00000419738.1 | n.1647C>T | non_coding_transcript_exon_variant | 2/3 | 2 | |||||
OR10R2 | ENST00000641400.1 | c.731G>A | p.Arg244Gln | missense_variant | 1/1 | A2 | |||
ENST00000426251.1 | n.217-5974C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251202Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135752
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461748Hom.: 0 Cov.: 32 AF XY: 0.000133 AC XY: 97AN XY: 727186
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152044Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2021 | The c.764G>A (p.R255Q) alteration is located in exon 1 (coding exon 1) of the OR10R2 gene. This alteration results from a G to A substitution at nucleotide position 764, causing the arginine (R) at amino acid position 255 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