1-248180551-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001004688.2(OR2M2):c.566G>A(p.Cys189Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,613,744 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 1 hom. )
Consequence
OR2M2
NM_001004688.2 missense
NM_001004688.2 missense
Scores
5
2
12
Clinical Significance
Conservation
PhyloP100: 2.92
Genes affected
OR2M2 (HGNC:8268): (olfactory receptor family 2 subfamily M 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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR2M2 | NM_001004688.2 | c.566G>A | p.Cys189Tyr | missense_variant | 2/2 | ENST00000641836.1 | NP_001004688.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR2M2 | ENST00000641836.1 | c.566G>A | p.Cys189Tyr | missense_variant | 2/2 | NM_001004688.2 | ENSP00000493201 | P1 | ||
OR2M2 | ENST00000641211.1 | c.566G>A | p.Cys189Tyr | missense_variant | 3/3 | ENSP00000492974 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152126Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251128Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135712
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GnomAD4 exome AF: 0.000154 AC: 225AN: 1461618Hom.: 1 Cov.: 72 AF XY: 0.000144 AC XY: 105AN XY: 727124
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GnomAD4 genome AF: 0.000105 AC: 16AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74310
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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 | Dec 05, 2022 | The c.566G>A (p.C189Y) alteration is located in exon 1 (coding exon 1) of the OR2M2 gene. This alteration results from a G to A substitution at nucleotide position 566, causing the cysteine (C) at amino acid position 189 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
.;.;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;H;H
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Pathogenic
.;.;D
REVEL
Benign
Sift
Pathogenic
.;.;D
Sift4G
Pathogenic
.;.;D
Polyphen
D;D;D
Vest4
0.14
MVP
0.30
MPC
0.68
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