rs6672995
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001004492.2(OR2B11):c.-3175C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,180 control chromosomes in the GnomAD database, including 1,956 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 0.15 ( 1956 hom., cov: 32)
Exomes 𝑓: 0.13 ( 0 hom. )
Consequence
OR2B11
NM_001004492.2 5_prime_UTR
NM_001004492.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.36
Genes affected
OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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=-0.79).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2B11 | NM_001004492.2 | c.-3175C>T | 5_prime_UTR_variant | 1/2 | ENST00000641149.2 | ||
OR2B11 | NR_169840.1 | n.278C>T | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2B11 | ENST00000641149.2 | c.-3175C>T | 5_prime_UTR_variant | 1/2 | NM_001004492.2 | P1 | |||
OR2B11 | ENST00000641527.1 | c.-1306C>T | 5_prime_UTR_variant | 1/3 | P1 | ||||
OR2B11 | ENST00000641613.1 | n.278C>T | non_coding_transcript_exon_variant | 1/5 |
Frequencies
GnomAD3 genomes ? AF: 0.149 AC: 22726AN: 152032Hom.: 1957 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.133 AC: 4AN: 30Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3AN XY: 22
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GnomAD4 genome ? AF: 0.149 AC: 22731AN: 152150Hom.: 1956 Cov.: 32 AF XY: 0.151 AC XY: 11260AN XY: 74362
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at