chr3-98169473-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005515.2(OR5H15):c.774G>A(p.Met258Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,612,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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.774G>A | p.Met258Ile | 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.774G>A | p.Met258Ile | missense_variant | 2/2 | NM_001005515.2 | ENSP00000493082 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151322Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250660Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135494
GnomAD4 exome AF: 0.0000630 AC: 92AN: 1461406Hom.: 0 Cov.: 34 AF XY: 0.0000523 AC XY: 38AN XY: 726996
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151434Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74036
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.774G>A (p.M258I) alteration is located in exon 1 (coding exon 1) of the OR5H15 gene. This alteration results from a G to A substitution at nucleotide position 774, causing the methionine (M) at amino acid position 258 to be replaced by an isoleucine (I). 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