11-6921480-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001004684.1(OR2D3):c.479T>C(p.Leu160Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,474 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004684.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR2D3 | NM_001004684.1 | c.479T>C | p.Leu160Pro | missense_variant | Exon 1 of 1 | ENST00000317834.5 | NP_001004684.1 | |
LOC107984019 | XR_001748111.2 | n.931+3018A>G | intron_variant | Intron 3 of 3 | ||||
LOC107984019 | XR_001748112.3 | n.1466+3018A>G | intron_variant | Intron 3 of 3 | ||||
LOC107984019 | XR_007062575.1 | n.980+3018A>G | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250792Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135506
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461474Hom.: 0 Cov.: 54 AF XY: 0.00000138 AC XY: 1AN XY: 727016
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.479T>C (p.L160P) alteration is located in exon 1 (coding exon 1) of the OR2D3 gene. This alteration results from a T to C substitution at nucleotide position 479, causing the leucine (L) at amino acid position 160 to be replaced by a proline (P). 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