3-98169013-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005515.2(OR5H15):c.314C>T(p.Ala105Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000799 in 1,613,516 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005515.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR5H15 | NM_001005515.2 | c.314C>T | p.Ala105Val | missense_variant | 2/2 | ENST00000641450.1 | NP_001005515.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR5H15 | ENST00000641450.1 | c.314C>T | p.Ala105Val | missense_variant | 2/2 | NM_001005515.2 | ENSP00000493082 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250796Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135544
GnomAD4 exome AF: 0.0000848 AC: 124AN: 1461452Hom.: 1 Cov.: 36 AF XY: 0.0000825 AC XY: 60AN XY: 727048
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.314C>T (p.A105V) alteration is located in exon 1 (coding exon 1) of the OR5H15 gene. This alteration results from a C to T substitution at nucleotide position 314, causing the alanine (A) at amino acid position 105 to be replaced by a valine (V). 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