1-247949404-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001963.1(OR2L8):āc.547A>Gā(p.Met183Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,614,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001001963.1 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 |
---|---|---|---|---|---|---|---|
OR2L8 | NM_001001963.1 | c.547A>G | p.Met183Val | missense_variant | 1/1 | ENST00000623922.1 | |
OR2L13 | NM_001304535.3 | c.-19+12020A>G | intron_variant | ||||
OR2L13 | NM_175911.5 | c.-144+12020A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2L8 | ENST00000623922.1 | c.547A>G | p.Met183Val | missense_variant | 1/1 | NM_001001963.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251230Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135768
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461848Hom.: 0 Cov.: 40 AF XY: 0.0000275 AC XY: 20AN XY: 727224
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2023 | The c.547A>G (p.M183V) alteration is located in exon 1 (coding exon 1) of the OR2L8 gene. This alteration results from a A to G substitution at nucleotide position 547, causing the methionine (M) at amino acid position 183 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