1-248638376-T-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001001827.2(OR2T35):āc.883A>Gā(p.Lys295Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00049 ( 0 hom., cov: 16)
Exomes š: 0.000068 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
OR2T35
NM_001001827.2 missense
NM_001001827.2 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
OR2T35 (HGNC:31257): (olfactory receptor family 2 subfamily T member 35) 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 -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.09043217).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000470 AC: 60AN: 127594Hom.: 0 Cov.: 16
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000676 AC: 62AN: 917170Hom.: 0 Cov.: 13 AF XY: 0.0000671 AC XY: 32AN XY: 477158
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GnomAD4 genome AF: 0.000485 AC: 62AN: 127718Hom.: 0 Cov.: 16 AF XY: 0.000392 AC XY: 24AN XY: 61276
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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 | Jun 11, 2021 | The c.883A>G (p.K295E) alteration is located in exon 1 (coding exon 1) of the OR2T35 gene. This alteration results from a A to G substitution at nucleotide position 883, causing the lysine (K) at amino acid position 295 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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
LIST_S2
Benign
.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
PrimateAI
Benign
T
PROVEAN
Uncertain
.;D
REVEL
Benign
Sift
Uncertain
.;D
Sift4G
Uncertain
.;D
Polyphen
P;P
Vest4
0.26
MVP
0.50
MPC
2.1
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