chr9-122629491-CA-C

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.75

Publications

17 publications found
Variant links:
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
OR1B1NM_001004450.3 linkc.41delT p.Leu14CysfsTer24 frameshift_variant Exon 2 of 2 NP_001004450.2 Q8NGR6
OR1B1NM_001409693.1 linkc.41delT p.Leu14CysfsTer24 frameshift_variant Exon 2 of 2 NP_001396622.1
LOC124902265XR_007061759.1 linkn.345-7605delA intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR1B1ENST00000623530.2 linkc.41delT p.Leu14CysfsTer24 frameshift_variant Exon 2 of 2 6 ENSP00000485577.2 Q8NGR6

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
6.86e-7
AC:
1
AN:
1457436
Hom.:
0
Cov.:
34
AF XY:
0.00000138
AC XY:
1
AN XY:
724930
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33308
American (AMR)
AF:
0.00
AC:
0
AN:
43978
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25916
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39668
South Asian (SAS)
AF:
0.0000117
AC:
1
AN:
85486
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53296
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5750
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1109818
Other (OTH)
AF:
0.00
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
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.7
Mutation Taster
=181/19
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11421222; hg19: chr9-125391770; API