rs17184009

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

Scores

2
4
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.70

Publications

13 publications found
Variant links:
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]

Genome browser will be placed here

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
OR10C1NM_013941.4 linkc.163C>T p.Gln55* stop_gained Exon 1 of 1 ENST00000444197.3 NP_039229.3 Q96KK4A0A126GV80
OR11A1NM_001394828.1 linkc.-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
OR10C1ENST00000444197.3 linkc.163C>T p.Gln55* stop_gained Exon 1 of 1 6 NM_013941.4 ENSP00000419119.1 Q96KK4
OR11A1ENST00000377149.5 linkc.-388-8191G>A intron_variant Intron 1 of 4 6 NM_001394828.1 ENSP00000366354.1 Q9GZK7
OR10C1ENST00000622521.1 linkc.169C>T p.Gln57* stop_gained Exon 1 of 1 6 ENSP00000481429.1 A0A087WY02

Frequencies

GnomAD3 genomes
AF:
0.0253
AC:
3852
AN:
152150
Hom.:
114
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0744
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0156
Gnomad ASJ
AF:
0.0222
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00166
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00551
Gnomad OTH
AF:
0.0330
GnomAD2 exomes
AF:
0.0109
AC:
2704
AN:
247104
AF XY:
0.00931
show subpopulations
Gnomad AFR exome
AF:
0.0804
Gnomad AMR exome
AF:
0.0140
Gnomad ASJ exome
AF:
0.0206
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000462
Gnomad NFE exome
AF:
0.00591
Gnomad OTH exome
AF:
0.0127
GnomAD4 exome
AF:
0.00697
AC:
10193
AN:
1461454
Hom.:
159
Cov.:
31
AF XY:
0.00667
AC XY:
4849
AN XY:
727042
show subpopulations
African (AFR)
AF:
0.0798
AC:
2671
AN:
33470
American (AMR)
AF:
0.0154
AC:
687
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
0.0213
AC:
558
AN:
26136
East Asian (EAS)
AF:
0.0000504
AC:
2
AN:
39700
South Asian (SAS)
AF:
0.00174
AC:
150
AN:
86258
European-Finnish (FIN)
AF:
0.000434
AC:
23
AN:
53016
Middle Eastern (MID)
AF:
0.0324
AC:
187
AN:
5768
European-Non Finnish (NFE)
AF:
0.00466
AC:
5178
AN:
1111992
Other (OTH)
AF:
0.0122
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:
3861
AN:
152268
Hom.:
115
Cov.:
32
AF XY:
0.0240
AC XY:
1785
AN XY:
74454
show subpopulations
African (AFR)
AF:
0.0744
AC:
3090
AN:
41532
American (AMR)
AF:
0.0155
AC:
237
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.0222
AC:
77
AN:
3472
East Asian (EAS)
AF:
0.000193
AC:
1
AN:
5174
South Asian (SAS)
AF:
0.00145
AC:
7
AN:
4822
European-Finnish (FIN)
AF:
0.0000941
AC:
1
AN:
10622
Middle Eastern (MID)
AF:
0.0136
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
0.00551
AC:
375
AN:
68026
Other (OTH)
AF:
0.0327
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:
0.0136
Hom.:
92
Bravo
AF:
0.0293
TwinsUK
AF:
0.00674
AC:
25
ALSPAC
AF:
0.00467
AC:
18
ESP6500AA
AF:
0.0778
AC:
235
ESP6500EA
AF:
0.00720
AC:
39
ExAC
AF:
0.0113
AC:
1355
Asia WGS
AF:
0.00751
AC:
26
AN:
3478
EpiCase
AF:
0.00687
EpiControl
AF:
0.00723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.22
D
BayesDel_noAF
Pathogenic
0.60
CADD
Pathogenic
39
DANN
Uncertain
1.0
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.27
FATHMM_MKL
Uncertain
0.84
D
PhyloP100
2.7
GERP RS
3.7
PromoterAI
0.0053
Neutral
Mutation Taster
=172/28
polymorphism (auto)

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: rs17184009; hg19: chr6-29407955; COSMIC: COSV105318044; API