14-19975855-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005486.2(OR4K15):c.265C>T(p.Arg89Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. R89S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005486.2 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: 0.0000593 AC: 9AN: 151886Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251270Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135816
GnomAD4 exome AF: 0.0000801 AC: 117AN: 1461518Hom.: 0 Cov.: 37 AF XY: 0.0000853 AC XY: 62AN XY: 727074
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152004Hom.: 0 Cov.: 31 AF XY: 0.0000808 AC XY: 6AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.337C>T (p.R113C) alteration is located in exon 1 (coding exon 1) of the OR4K15 gene. This alteration results from a C to T substitution at nucleotide position 337, causing the arginine (R) at amino acid position 113 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