rs16895070
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001396058.1(OR2I1P):āc.562T>Cā(p.Cys188Arg) variant causes a missense change. The variant allele was found at a frequency of 0.099 in 398,526 control chromosomes in the GnomAD database, including 5,850 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 0.16 ( 4410 hom., cov: 33)
Exomes š: 0.063 ( 1440 hom. )
Consequence
OR2I1P
NM_001396058.1 missense
NM_001396058.1 missense
Scores
1
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.60
Genes affected
OR2I1P (HGNC:8258): (olfactory receptor family 2 subfamily I member 1 pseudogene) 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 (MetaRNN=0.0016171038).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2I1P | NM_001396058.1 | c.562T>C | p.Cys188Arg | missense_variant | 2/2 | ENST00000641137.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2I1P | ENST00000641137.2 | c.562T>C | p.Cys188Arg | missense_variant | 2/2 | NM_001396058.1 | P1 | ||
OR2I1P | ENST00000641730.1 | n.1424T>C | non_coding_transcript_exon_variant | 2/2 | |||||
OR2I1P | ENST00000642037.1 | n.750T>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23952AN: 152176Hom.: 4378 Cov.: 33
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GnomAD4 exome AF: 0.0627 AC: 15440AN: 246232Hom.: 1440 Cov.: 0 AF XY: 0.0595 AC XY: 7423AN XY: 124782
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GnomAD4 genome ? AF: 0.158 AC: 24029AN: 152294Hom.: 4410 Cov.: 33 AF XY: 0.156 AC XY: 11619AN XY: 74474
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477
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at