11-5947891-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001003443.3(OR56A3):āc.545T>Cā(p.Ile182Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000554 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.000055 ( 0 hom. )
Consequence
OR56A3
NM_001003443.3 missense
NM_001003443.3 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 0.0160
Genes affected
OR56A3 (HGNC:14786): (olfactory receptor family 56 subfamily A member 3) 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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.36374065).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR56A3 | NM_001003443.3 | c.545T>C | p.Ile182Thr | missense_variant | 3/3 | ENST00000641160.1 | NP_001003443.2 | |
OR56A3 | XM_047426926.1 | c.545T>C | p.Ile182Thr | missense_variant | 3/6 | XP_047282882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR56A3 | ENST00000641160.1 | c.545T>C | p.Ile182Thr | missense_variant | 3/3 | NM_001003443.3 | ENSP00000493059.1 | |||
OR56A3 | ENST00000641905.1 | c.545T>C | p.Ile182Thr | missense_variant | 4/4 | ENSP00000493319.1 | ||||
OR56A3 | ENST00000641878.1 | n.402-796T>C | intron_variant |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250106Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135638
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GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461886Hom.: 0 Cov.: 36 AF XY: 0.0000633 AC XY: 46AN XY: 727240
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GnomAD4 genome Cov.: 33
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Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.545T>C (p.I182T) alteration is located in exon 1 (coding exon 1) of the OR56A3 gene. This alteration results from a T to C substitution at nucleotide position 545, causing the isoleucine (I) at amino acid position 182 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
PrimateAI
Benign
T
PROVEAN
Uncertain
.;.;D
REVEL
Benign
Sift
Uncertain
.;.;D
Sift4G
Uncertain
.;.;D
Polyphen
P;P;P
Vest4
0.26
MVP
0.62
MPC
0.23
ClinPred
D
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