11-4367830-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005161.3(OR52B4):c.466G>A(p.Gly156Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,482 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_001005161.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR52B4 | NM_001005161.3 | c.466G>A | p.Gly156Ser | missense_variant | Exon 1 of 1 | ENST00000624801.3 | NP_001005161.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248878Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134996
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461456Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727070
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466G>A (p.G156S) alteration is located in exon 1 (coding exon 1) of the OR52B4 gene. This alteration results from a G to A substitution at nucleotide position 466, causing the glycine (G) at amino acid position 156 to be replaced by a serine (S). 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