rs1902318
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001004755.2(OR51L1):c.*2979G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,990 control chromosomes in the GnomAD database, including 6,633 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.29 ( 6632 hom., cov: 31)
Exomes 𝑓: 0.29 ( 1 hom. )
Consequence
OR51L1
NM_001004755.2 3_prime_UTR
NM_001004755.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.137
Genes affected
OR51L1 (HGNC:14759): (olfactory receptor family 51 subfamily L 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. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR51L1 | NM_001004755.2 | c.*2979G>A | 3_prime_UTR_variant | 3/3 | ENST00000641819.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR51L1 | ENST00000641819.1 | c.*2979G>A | 3_prime_UTR_variant | 3/3 | NM_001004755.2 | P1 | |||
OR51L1 | ENST00000641624.1 | n.926G>A | non_coding_transcript_exon_variant | 3/4 | |||||
OR51L1 | ENST00000642056.1 | n.926G>A | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.289 AC: 43841AN: 151854Hom.: 6628 Cov.: 31
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GnomAD4 exome AF: 0.286 AC: 4AN: 14Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 4AN XY: 12
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GnomAD4 genome ? AF: 0.289 AC: 43871AN: 151976Hom.: 6632 Cov.: 31 AF XY: 0.285 AC XY: 21178AN XY: 74276
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at