rs17184009
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_013941.4(OR10C1):c.163C>T(p.Gln55*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00871 in 1,613,722 control chromosomes in the GnomAD database, including 274 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.025 ( 115 hom., cov: 32)
Exomes 𝑓: 0.0070 ( 159 hom. )
Consequence
OR10C1
NM_013941.4 stop_gained
NM_013941.4 stop_gained
Scores
2
4
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.70
Publications
13 publications found
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 was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR10C1 | NM_013941.4 | c.163C>T | p.Gln55* | stop_gained | Exon 1 of 1 | ENST00000444197.3 | NP_039229.3 | |
OR11A1 | NM_001394828.1 | c.-388-8191G>A | intron_variant | Intron 1 of 4 | ENST00000377149.5 | NP_001381757.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR10C1 | ENST00000444197.3 | c.163C>T | p.Gln55* | stop_gained | Exon 1 of 1 | 6 | NM_013941.4 | ENSP00000419119.1 | ||
OR11A1 | ENST00000377149.5 | c.-388-8191G>A | intron_variant | Intron 1 of 4 | 6 | NM_001394828.1 | ENSP00000366354.1 | |||
OR10C1 | ENST00000622521.1 | c.169C>T | p.Gln57* | stop_gained | Exon 1 of 1 | 6 | ENSP00000481429.1 |
Frequencies
GnomAD3 genomes AF: 0.0253 AC: 3852AN: 152150Hom.: 114 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3852
AN:
152150
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0109 AC: 2704AN: 247104 AF XY: 0.00931 show subpopulations
GnomAD2 exomes
AF:
AC:
2704
AN:
247104
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00697 AC: 10193AN: 1461454Hom.: 159 Cov.: 31 AF XY: 0.00667 AC XY: 4849AN XY: 727042 show subpopulations
GnomAD4 exome
AF:
AC:
10193
AN:
1461454
Hom.:
Cov.:
31
AF XY:
AC XY:
4849
AN XY:
727042
show subpopulations
African (AFR)
AF:
AC:
2671
AN:
33470
American (AMR)
AF:
AC:
687
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
558
AN:
26136
East Asian (EAS)
AF:
AC:
2
AN:
39700
South Asian (SAS)
AF:
AC:
150
AN:
86258
European-Finnish (FIN)
AF:
AC:
23
AN:
53016
Middle Eastern (MID)
AF:
AC:
187
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
5178
AN:
1111992
Other (OTH)
AF:
AC:
737
AN:
60390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.465
Heterozygous variant carriers
0
623
1246
1868
2491
3114
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
232
464
696
928
1160
<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 AF: 0.0254 AC: 3861AN: 152268Hom.: 115 Cov.: 32 AF XY: 0.0240 AC XY: 1785AN XY: 74454 show subpopulations
GnomAD4 genome
AF:
AC:
3861
AN:
152268
Hom.:
Cov.:
32
AF XY:
AC XY:
1785
AN XY:
74454
show subpopulations
African (AFR)
AF:
AC:
3090
AN:
41532
American (AMR)
AF:
AC:
237
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
77
AN:
3472
East Asian (EAS)
AF:
AC:
1
AN:
5174
South Asian (SAS)
AF:
AC:
7
AN:
4822
European-Finnish (FIN)
AF:
AC:
1
AN:
10622
Middle Eastern (MID)
AF:
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
AC:
375
AN:
68026
Other (OTH)
AF:
AC:
69
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
184
369
553
738
922
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
40
80
120
160
200
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
25
ALSPAC
AF:
AC:
18
ESP6500AA
AF:
AC:
235
ESP6500EA
AF:
AC:
39
ExAC
AF:
AC:
1355
Asia WGS
AF:
AC:
26
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
PhyloP100
GERP RS
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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