9-104598683-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004482.1(OR13C5):c.731G>T(p.Arg244Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000545 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. R244H) has been classified as Likely benign.
Frequency
Consequence
NM_001004482.1 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 |
---|---|---|---|---|---|---|---|
OR13C5 | NM_001004482.1 | c.731G>T | p.Arg244Leu | missense_variant | 1/1 | ENST00000374779.3 | |
LOC107987105 | XR_007061705.1 | n.427+23347G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13C5 | ENST00000374779.3 | c.731G>T | p.Arg244Leu | missense_variant | 1/1 | NM_001004482.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250762Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135462
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461664Hom.: 0 Cov.: 54 AF XY: 0.0000413 AC XY: 30AN XY: 727136
GnomAD4 genome AF: 0.000230 AC: 35AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.731G>T (p.R244L) alteration is located in exon 1 (coding exon 1) of the OR13C5 gene. This alteration results from a G to T substitution at nucleotide position 731, causing the arginine (R) at amino acid position 244 to be replaced by a leucine (L). 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