rs200877558
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001004695.2(OR2T33):āc.479T>Cā(p.Val160Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.039 ( 17 hom., cov: 33)
Exomes š: 0.24 ( 66 hom. )
Failed GnomAD Quality Control
Consequence
OR2T33
NM_001004695.2 missense
NM_001004695.2 missense
Scores
13
Clinical Significance
Conservation
PhyloP100: -1.73
Genes affected
OR2T33 (HGNC:31255): (olfactory receptor family 2 subfamily T member 33) 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 made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0024973452).
BP6
?
Variant 1-248273336-A-G is Benign according to our data. Variant chr1-248273336-A-G is described in ClinVar as [Benign]. Clinvar id is 403272.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2T33 | NM_001004695.2 | c.479T>C | p.Val160Ala | missense_variant | 2/2 | ENST00000641220.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2T33 | ENST00000641220.1 | c.479T>C | p.Val160Ala | missense_variant | 2/2 | NM_001004695.2 | P1 | ||
OR2T33 | ENST00000318021.4 | c.479T>C | p.Val160Ala | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 4268AN: 110592Hom.: 16 Cov.: 33 FAILED QC
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?
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.244 AC: 211383AN: 865754Hom.: 66 Cov.: 121 AF XY: 0.235 AC XY: 101799AN XY: 432548
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Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0387 AC: 4279AN: 110664Hom.: 17 Cov.: 33 AF XY: 0.0408 AC XY: 2202AN XY: 53960
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N
PrimateAI
Benign
T
Polyphen
B;B
Vest4
0.056
MPC
1.3
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at