chr1-248650410-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001824.2(OR2T27):c.475C>T(p.Leu159Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000852 in 1,396,584 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_001001824.2 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 |
---|---|---|---|---|---|---|---|
OR2T27 | NM_001001824.2 | c.475C>T | p.Leu159Phe | missense_variant | 2/2 | ENST00000460972.4 | |
OR2T27 | NM_001386060.1 | c.475C>T | p.Leu159Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2T27 | ENST00000460972.4 | c.475C>T | p.Leu159Phe | missense_variant | 2/2 | NM_001001824.2 | P1 | ||
OR2T27 | ENST00000641652.1 | c.475C>T | p.Leu159Phe | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000423 AC: 54AN: 127600Hom.: 0 Cov.: 17
GnomAD3 exomes AF: 0.000104 AC: 22AN: 212272Hom.: 0 AF XY: 0.0000871 AC XY: 10AN XY: 114868
GnomAD4 exome AF: 0.0000489 AC: 62AN: 1268888Hom.: 0 Cov.: 23 AF XY: 0.0000469 AC XY: 30AN XY: 639064
GnomAD4 genome AF: 0.000446 AC: 57AN: 127696Hom.: 0 Cov.: 17 AF XY: 0.000545 AC XY: 33AN XY: 60578
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.475C>T (p.L159F) alteration is located in exon 1 (coding exon 1) of the OR2T27 gene. This alteration results from a C to T substitution at nucleotide position 475, causing the leucine (L) at amino acid position 159 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