chr11-58358583-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001005489.2(OR5B17):c.487C>A(p.Arg163Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,076 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001005489.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR5B17 | NM_001005489.2 | c.487C>A | p.Arg163Ser | missense_variant | 1/1 | ENST00000357377.3 | NP_001005489.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR5B17 | ENST00000357377.3 | c.487C>A | p.Arg163Ser | missense_variant | 1/1 | NM_001005489.2 | ENSP00000349945 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250968Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135602
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461806Hom.: 2 Cov.: 35 AF XY: 0.0000165 AC XY: 12AN XY: 727198
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | 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