chr9-122629491-CA-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The ENST00000623530.2(OR1B1):c.41delT(p.Leu14CysfsTer24) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000686 in 1,457,436 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
OR1B1
ENST00000623530.2 frameshift
ENST00000623530.2 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.75
Publications
17 publications found
Genes affected
OR1B1 (HGNC:8181): (olfactory receptor family 1 subfamily B 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, Jun 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR1B1 | NM_001004450.3 | c.41delT | p.Leu14CysfsTer24 | frameshift_variant | Exon 2 of 2 | NP_001004450.2 | ||
OR1B1 | NM_001409693.1 | c.41delT | p.Leu14CysfsTer24 | frameshift_variant | Exon 2 of 2 | NP_001396622.1 | ||
LOC124902265 | XR_007061759.1 | n.345-7605delA | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457436Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 724930 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1457436
Hom.:
Cov.:
34
AF XY:
AC XY:
1
AN XY:
724930
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33308
American (AMR)
AF:
AC:
0
AN:
43978
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25916
East Asian (EAS)
AF:
AC:
0
AN:
39668
South Asian (SAS)
AF:
AC:
1
AN:
85486
European-Finnish (FIN)
AF:
AC:
0
AN:
53296
Middle Eastern (MID)
AF:
AC:
0
AN:
5750
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1109818
Other (OTH)
AF:
AC:
0
AN:
60216
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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30-35
35-40
40-45
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>80
Age
GnomAD4 genome Cov.: 0
GnomAD4 genome
Cov.:
0
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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