rs10946991
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_013941.4(OR10C1):āc.762A>Cā(p.Ala254=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 1,613,382 control chromosomes in the GnomAD database, including 3,737 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: š 0.098 ( 1350 hom., cov: 32)
Exomes š: 0.041 ( 2387 hom. )
Consequence
OR10C1
NM_013941.4 synonymous
NM_013941.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.87
Genes affected
OR10C1 (HGNC:8165): (olfactory receptor family 10 subfamily C 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]
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP7
Synonymous conserved (PhyloP=-1.87 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR10C1 | NM_013941.4 | c.762A>C | p.Ala254= | synonymous_variant | 1/1 | ENST00000444197.3 | NP_039229.3 | |
OR11A1 | NM_001394828.1 | c.-388-8790T>G | intron_variant | ENST00000377149.5 | NP_001381757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR10C1 | ENST00000444197.3 | c.762A>C | p.Ala254= | synonymous_variant | 1/1 | NM_013941.4 | ENSP00000419119 | P1 | ||
OR11A1 | ENST00000377149.5 | c.-388-8790T>G | intron_variant | NM_001394828.1 | ENSP00000366354 | P1 | ||||
OR10C1 | ENST00000622521.1 | c.768A>C | p.Ala256= | synonymous_variant | 1/1 | ENSP00000481429 |
Frequencies
GnomAD3 genomes AF: 0.0977 AC: 14829AN: 151794Hom.: 1340 Cov.: 32
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GnomAD3 exomes AF: 0.0555 AC: 13783AN: 248482Hom.: 761 AF XY: 0.0508 AC XY: 6853AN XY: 134872
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GnomAD4 exome AF: 0.0408 AC: 59689AN: 1461470Hom.: 2387 Cov.: 34 AF XY: 0.0407 AC XY: 29567AN XY: 727080
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GnomAD4 genome AF: 0.0978 AC: 14863AN: 151912Hom.: 1350 Cov.: 32 AF XY: 0.0948 AC XY: 7034AN XY: 74232
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at