chr3-98169357-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001005515.2(OR5H15):āc.658T>Cā(p.Phe220Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,613,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001005515.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR5H15 | NM_001005515.2 | c.658T>C | p.Phe220Leu | 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.658T>C | p.Phe220Leu | missense_variant | 2/2 | NM_001005515.2 | ENSP00000493082 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250284Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135306
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1460970Hom.: 0 Cov.: 34 AF XY: 0.0000372 AC XY: 27AN XY: 726780
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74312
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at