11-7825404-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_153445.2(OR5P3):c.569C>T(p.Ser190Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,682 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 (★).
Frequency
Consequence
NM_153445.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR5P3 | NM_153445.2 | c.569C>T | p.Ser190Phe | missense_variant | 2/2 | ENST00000641167.1 | NP_703146.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR5P3 | ENST00000641167.1 | c.569C>T | p.Ser190Phe | missense_variant | 2/2 | NM_153445.2 | ENSP00000492944.1 | |||
ENSG00000271758 | ENST00000527565.1 | n.542+53603C>T | intron_variant | 3 | ||||||
ENSG00000254951 | ENST00000529488.5 | n.531+53603C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461682Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727164
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2024 | The c.569C>T (p.S190F) alteration is located in exon 1 (coding exon 1) of the OR5P3 gene. This alteration results from a C to T substitution at nucleotide position 569, causing the serine (S) at amino acid position 190 to be replaced by a phenylalanine (F). 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