1-248061438-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004687.2(OR2L3):c.757C>A(p.Pro253Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,614,052 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
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.757C>A | p.Pro253Thr | missense_variant | 2/2 | ENST00000359959.4 | NP_001004687.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR2L3 | ENST00000359959.4 | c.757C>A | p.Pro253Thr | missense_variant | 2/2 | 6 | NM_001004687.2 | ENSP00000353044.3 | ||
OR2L3 | ENST00000641161.1 | c.757C>A | p.Pro253Thr | missense_variant | 2/2 | ENSP00000493424.1 | ||||
OR2L3 | ENST00000641649.1 | c.757C>A | p.Pro253Thr | missense_variant | 3/3 | ENSP00000493020.1 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152072Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251400Hom.: 0 AF XY: 0.000353 AC XY: 48AN XY: 135878
GnomAD4 exome AF: 0.000124 AC: 181AN: 1461862Hom.: 1 Cov.: 37 AF XY: 0.000172 AC XY: 125AN XY: 727232
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152190Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 02, 2024 | The c.757C>A (p.P253T) alteration is located in exon 1 (coding exon 1) of the OR2L3 gene. This alteration results from a C to A substitution at nucleotide position 757, causing the proline (P) at amino acid position 253 to be replaced by a threonine (T). 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