11-5857285-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005168.3(OR52E8):āc.406A>Gā(p.Met136Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000822 in 1,460,552 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_001005168.3 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 |
---|---|---|---|---|---|---|---|---|
OR52E8 | NM_001005168.3 | c.406A>G | p.Met136Val | missense_variant | 1/1 | ENST00000537935.2 | NP_001005168.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR52E8 | ENST00000537935.2 | c.406A>G | p.Met136Val | missense_variant | 1/1 | 6 | NM_001005168.3 | ENSP00000444054.2 | ||
TRIM5 | ENST00000412903.1 | c.-62+80116A>G | intron_variant | 1 | ENSP00000388031.1 | |||||
TRIM5 | ENST00000380027.5 | c.-543-1431A>G | intron_variant | 5 | ENSP00000369366.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250536Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135492
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460552Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 726682
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.418A>G (p.M140V) alteration is located in exon 1 (coding exon 1) of the OR52E8 gene. This alteration results from a A to G substitution at nucleotide position 418, causing the methionine (M) at amino acid position 140 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