11-5422658-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004757.2(OR51Q1):c.458G>T(p.Cys153Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C153R) has been classified as Likely benign.
Frequency
Consequence
NM_001004757.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR51Q1 | NM_001004757.2 | c.458G>T | p.Cys153Phe | missense_variant | 1/1 | ENST00000300778.4 | NP_001004757.1 | |
OR51B5 | NM_001005567.3 | c.-359-75748C>A | intron_variant | NP_001005567.2 | ||||
OR51B5 | NR_038321.2 | n.85-75748C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR51Q1 | ENST00000300778.4 | c.458G>T | p.Cys153Phe | missense_variant | 1/1 | 6 | NM_001004757.2 | ENSP00000300778.4 | ||
ENSG00000239920 | ENST00000380259.7 | n.*740-76759C>A | intron_variant | 5 | ENSP00000369609.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251454Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135896
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461826Hom.: 0 Cov.: 45 AF XY: 0.0000413 AC XY: 30AN XY: 727214
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.458G>T (p.C153F) alteration is located in exon 1 (coding exon 1) of the OR51Q1 gene. This alteration results from a G to T substitution at nucleotide position 458, causing the cysteine (C) at amino acid position 153 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