rs10946990
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394828.1(OR11A1):c.-92+44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 778,464 control chromosomes in the GnomAD database, including 29,331 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 0.22 ( 4090 hom., cov: 29)
Exomes 𝑓: 0.28 ( 25241 hom. )
Consequence
OR11A1
NM_001394828.1 intron
NM_001394828.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.06
Genes affected
OR11A1 (HGNC:8176): (olfactory receptor family 11 subfamily A 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]
OR5V1 (HGNC:13972): (olfactory receptor family 5 subfamily V 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=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR11A1 | NM_001394828.1 | c.-92+44A>G | intron_variant | ENST00000377149.5 | |||
OR11A1 | NM_013937.4 | c.-91-1137A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR11A1 | ENST00000377149.5 | c.-92+44A>G | intron_variant | NM_001394828.1 | P1 | ||||
OR5V1 | ENST00000377154.1 | c.-197+2995A>G | intron_variant | P1 | |||||
OR11A1 | ENST00000641152.2 | c.-91-1137A>G | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.220 AC: 33221AN: 150828Hom.: 4091 Cov.: 29
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GnomAD4 exome AF: 0.281 AC: 176045AN: 627552Hom.: 25241 Cov.: 8 AF XY: 0.280 AC XY: 82112AN XY: 293238
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GnomAD4 genome ? AF: 0.220 AC: 33223AN: 150912Hom.: 4090 Cov.: 29 AF XY: 0.219 AC XY: 16130AN XY: 73652
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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