rs79869455
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001004476.2(OR10K2):āc.116T>Gā(p.Leu39Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00157 in 1,613,768 control chromosomes in the GnomAD database, including 41 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: š 0.0081 ( 18 hom., cov: 31)
Exomes š: 0.00089 ( 23 hom. )
Consequence
OR10K2
NM_001004476.2 missense
NM_001004476.2 missense
Scores
1
4
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.02
Genes affected
OR10K2 (HGNC:14826): (olfactory receptor family 10 subfamily K member 2) 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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0049262643).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00812 (1236/152176) while in subpopulation AFR AF= 0.0286 (1186/41536). AF 95% confidence interval is 0.0272. There are 18 homozygotes in gnomad4. There are 548 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR10K2 | NM_001004476.2 | c.116T>G | p.Leu39Arg | missense_variant | 2/2 | ENST00000641042.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR10K2 | ENST00000641042.1 | c.116T>G | p.Leu39Arg | missense_variant | 2/2 | NM_001004476.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00812 AC: 1234AN: 152058Hom.: 18 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
1234
AN:
152058
Hom.:
Cov.:
31
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:
GnomAD3 exomes AF: 0.00212 AC: 532AN: 251120Hom.: 9 AF XY: 0.00151 AC XY: 205AN XY: 135714
GnomAD3 exomes
AF:
AC:
532
AN:
251120
Hom.:
AF XY:
AC XY:
205
AN XY:
135714
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000893 AC: 1305AN: 1461592Hom.: 23 Cov.: 33 AF XY: 0.000761 AC XY: 553AN XY: 727098
GnomAD4 exome
AF:
AC:
1305
AN:
1461592
Hom.:
Cov.:
33
AF XY:
AC XY:
553
AN XY:
727098
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00812 AC: 1236AN: 152176Hom.: 18 Cov.: 31 AF XY: 0.00737 AC XY: 548AN XY: 74402
GnomAD4 genome
?
AF:
AC:
1236
AN:
152176
Hom.:
Cov.:
31
AF XY:
AC XY:
548
AN XY:
74402
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
114
ESP6500EA
AF:
AC:
2
ExAC
?
AF:
AC:
289
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;H
MutationTaster
Benign
N
PrimateAI
Benign
T
Polyphen
D;D
Vest4
0.81
MVP
0.63
MPC
0.032
ClinPred
T
GERP RS
Varity_R
gMVP
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