11-5884662-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001005165.2(OR52E4):c.370C>T(p.Arg124Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00021 in 1,613,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R124H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005165.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250446Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135338
GnomAD4 exome AF: 0.000221 AC: 323AN: 1461332Hom.: 0 Cov.: 33 AF XY: 0.000219 AC XY: 159AN XY: 726988
GnomAD4 genome AF: 0.0000987 AC: 15AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.370C>T (p.R124C) alteration is located in exon 1 (coding exon 1) of the OR52E4 gene. This alteration results from a C to T substitution at nucleotide position 370, causing the arginine (R) at amino acid position 124 to be replaced by a cysteine (C). 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