rs1159032787
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001004696.2(OR2T4):c.660C>G(p.Ser220Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000855 in 116,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000086 ( 0 hom., cov: 32)
Consequence
OR2T4
NM_001004696.2 missense
NM_001004696.2 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: -4.07
Publications
1 publications found
Genes affected
OR2T4 (HGNC:15016): (olfactory receptor family 2 subfamily T member 4) 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: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001004696.2. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.00000855 AC: 1AN: 116922Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
116922
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:
GnomAD4 exome Cov.: 68
GnomAD4 exome
Cov.:
68
GnomAD4 genome 0.00000855 AC: 1AN: 116922Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 57098 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
116922
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
57098
show subpopulations
African (AFR)
AF:
AC:
1
AN:
35316
American (AMR)
AF:
AC:
0
AN:
11862
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2590
East Asian (EAS)
AF:
AC:
0
AN:
4536
South Asian (SAS)
AF:
AC:
0
AN:
3764
European-Finnish (FIN)
AF:
AC:
0
AN:
8014
Middle Eastern (MID)
AF:
AC:
0
AN:
244
European-Non Finnish (NFE)
AF:
AC:
0
AN:
48568
Other (OTH)
AF:
AC:
0
AN:
1582
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MutPred
Gain of helix (P = 0.0861)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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