1-248060763-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004687.2(OR2L3):āc.82A>Gā(p.Ile28Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,840 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 (ā ).
Frequency
Consequence
NM_001004687.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR2L3 | NM_001004687.2 | c.82A>G | p.Ile28Val | missense_variant | 2/2 | ENST00000359959.4 | NP_001004687.1 | |
LOC105373275 | XR_949369.3 | n.418+4373T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR2L3 | ENST00000359959.4 | c.82A>G | p.Ile28Val | missense_variant | 2/2 | NM_001004687.2 | ENSP00000353044 | P1 | ||
OR2L3 | ENST00000641161.1 | c.82A>G | p.Ile28Val | missense_variant | 2/2 | ENSP00000493424 | P1 | |||
OR2L3 | ENST00000641649.1 | c.82A>G | p.Ile28Val | missense_variant | 3/3 | ENSP00000493020 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251404Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135882
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461814Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727224
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.82A>G (p.I28V) alteration is located in exon 1 (coding exon 1) of the OR2L3 gene. This alteration results from a A to G substitution at nucleotide position 82, causing the isoleucine (I) at amino acid position 28 to be replaced by a valine (V). 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