11-59365282-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004729.2(OR5AN1):c.824C>T(p.Ala275Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,611,168 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 (★).
Frequency
Consequence
NM_001004729.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR5AN1 | NM_001004729.2 | c.824C>T | p.Ala275Val | missense_variant | Exon 2 of 2 | ENST00000641998.1 | NP_001004729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR5AN1 | ENST00000641998.1 | c.824C>T | p.Ala275Val | missense_variant | Exon 2 of 2 | NM_001004729.2 | ENSP00000493250.1 | |||
OR5AN1 | ENST00000313940.2 | c.824C>T | p.Ala275Val | missense_variant | Exon 1 of 1 | 6 | ENSP00000320302.2 | |||
OR5AN1 | ENST00000641850.1 | c.824C>T | p.Ala275Val | missense_variant | Exon 2 of 2 | ENSP00000492957.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250864Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135580
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459014Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726036
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.824C>T (p.A275V) alteration is located in exon 1 (coding exon 1) of the OR5AN1 gene. This alteration results from a C to T substitution at nucleotide position 824, causing the alanine (A) at amino acid position 275 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