NM_001005169.1:c.175C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005169.1(OR52I1):c.175C>T(p.Arg59Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000266 in 1,614,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R59Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005169.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152076Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000366 AC: 92AN: 251298Hom.: 1 AF XY: 0.000339 AC XY: 46AN XY: 135816
GnomAD4 exome AF: 0.000252 AC: 368AN: 1461846Hom.: 1 Cov.: 56 AF XY: 0.000248 AC XY: 180AN XY: 727226
GnomAD4 genome AF: 0.000401 AC: 61AN: 152192Hom.: 0 Cov.: 31 AF XY: 0.000470 AC XY: 35AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.175C>T (p.R59W) alteration is located in exon 1 (coding exon 1) of the OR52I1 gene. This alteration results from a C to T substitution at nucleotide position 175, causing the arginine (R) at amino acid position 59 to be replaced by a tryptophan (W). 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