chr11-58422513-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005566.3(OR5B2):c.749A>T(p.Tyr250Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005566.3 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 | UniProt |
---|---|---|---|---|---|---|---|
OR5B2 | NM_001005566.3 | c.749A>T | p.Tyr250Phe | missense_variant | 3/3 | ENST00000641342.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR5B2 | ENST00000641342.2 | c.749A>T | p.Tyr250Phe | missense_variant | 3/3 | NM_001005566.3 | P1 | ||
OR5B2 | ENST00000302581.2 | c.749A>T | p.Tyr250Phe | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250882Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135564
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461574Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727082
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.749A>T (p.Y250F) alteration is located in exon 1 (coding exon 1) of the OR5B2 gene. This alteration results from a A to T substitution at nucleotide position 749, causing the tyrosine (Y) at amino acid position 250 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