rs10838851
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001004726.1(OR4X1):c.819T>A(p.Tyr273Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,613,266 control chromosomes in the GnomAD database, including 435,620 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.69 ( 36959 hom., cov: 33)
Exomes 𝑓: 0.73 ( 398661 hom. )
Consequence
OR4X1
NM_001004726.1 stop_gained
NM_001004726.1 stop_gained
Scores
1
2
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.25
Genes affected
OR4X1 (HGNC:14854): (olfactory receptor family 4 subfamily X member 1) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR4X1 | NM_001004726.1 | c.819T>A | p.Tyr273Ter | stop_gained | 1/1 | ENST00000320048.1 | NP_001004726.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR4X1 | ENST00000320048.1 | c.819T>A | p.Tyr273Ter | stop_gained | 1/1 | NM_001004726.1 | ENSP00000321506 | P1 |
Frequencies
GnomAD3 genomes AF: 0.690 AC: 104863AN: 152022Hom.: 36946 Cov.: 33
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GnomAD3 exomes AF: 0.710 AC: 178267AN: 250956Hom.: 64742 AF XY: 0.701 AC XY: 94996AN XY: 135606
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GnomAD4 exome AF: 0.735 AC: 1073912AN: 1461126Hom.: 398661 Cov.: 40 AF XY: 0.729 AC XY: 530178AN XY: 726918
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GnomAD4 genome AF: 0.690 AC: 104914AN: 152140Hom.: 36959 Cov.: 33 AF XY: 0.689 AC XY: 51251AN XY: 74382
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Not reported inComputational scores
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BayesDel_addAF
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D
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DANN
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Benign
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Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
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Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at