1-248473609-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001005495.1(OR2T3):c.259C>T(p.Leu87Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,455,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005495.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR2T3 | NM_001005495.1 | c.259C>T | p.Leu87Phe | missense_variant | Exon 1 of 1 | ENST00000359594.3 | NP_001005495.1 | |
LOC105373279 | XR_007067006.1 | n.136-3450G>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 26
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1455524Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 724296
GnomAD4 genome Cov.: 26
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.259C>T (p.L87F) alteration is located in exon 1 (coding exon 1) of the OR2T3 gene. This alteration results from a C to T substitution at nucleotide position 259, causing the leucine (L) at amino acid position 87 to be replaced by a phenylalanine (F). 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
Publications
No publications associated with this variant yet.