1-248488771-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001004697.2(OR2T5):ā€‹c.183C>Gā€‹(p.Ser61Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 14)
Exomes š‘“: 0.0000046 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR2T5
NM_001004697.2 missense

Scores

14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.68
Variant links:
Genes affected
OR2T5 (HGNC:15017): (olfactory receptor family 2 subfamily T member 5) 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.23124719).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR2T5NM_001004697.2 linkuse as main transcriptc.183C>G p.Ser61Arg missense_variant 1/1 ENST00000641363.1
LOC105373277XR_002958498.2 linkuse as main transcriptn.188-3287G>C intron_variant, non_coding_transcript_variant
LOC105373277XR_001738575.2 linkuse as main transcriptn.144-3287G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR2T5ENST00000641363.1 linkuse as main transcriptc.183C>G p.Ser61Arg missense_variant 1/1 NM_001004697.2 P1

Frequencies

GnomAD3 genomes
Cov.:
14
GnomAD3 exomes
AF:
0.00000429
AC:
1
AN:
233368
Hom.:
0
AF XY:
0.00000787
AC XY:
1
AN XY:
127022
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000918
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000462
AC:
6
AN:
1299700
Hom.:
0
Cov.:
22
AF XY:
0.00000611
AC XY:
4
AN XY:
654484
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000616
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
14

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 submitterclinical testingAmbry GeneticsMar 29, 2022The c.183C>G (p.S61R) alteration is located in exon 1 (coding exon 1) of the OR2T5 gene. This alteration results from a C to G substitution at nucleotide position 183, causing the serine (S) at amino acid position 61 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.25
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
6.1
DANN
Benign
0.89
DEOGEN2
Benign
0.0056
T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.0036
N
M_CAP
Benign
0.00054
T
MetaRNN
Benign
0.23
T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
1.5
L
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.29
T
Polyphen
0.0
B
MutPred
0.74
Loss of catalytic residue at H60 (P = 0.1553);
ClinPred
0.064
T
GERP RS
-5.3
Varity_R
0.15
gMVP
0.098

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1161068370; hg19: chr1-248652072; API