chr19-15728311-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013939.2(OR10H2):c.268C>T(p.Arg90Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,612,256 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013939.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR10H2 | NM_013939.2 | c.268C>T | p.Arg90Cys | missense_variant | 1/1 | ENST00000305899.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR10H2 | ENST00000305899.5 | c.268C>T | p.Arg90Cys | missense_variant | 1/1 | NM_013939.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000489 AC: 12AN: 245612Hom.: 0 AF XY: 0.0000453 AC XY: 6AN XY: 132466
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1459880Hom.: 0 Cov.: 90 AF XY: 0.0000592 AC XY: 43AN XY: 726036
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152376Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.268C>T (p.R90C) alteration is located in exon 1 (coding exon 1) of the OR10H2 gene. This alteration results from a C to T substitution at nucleotide position 268, causing the arginine (R) at amino acid position 90 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