1-248488787-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001004697.2(OR2T5):ā€‹c.199A>Gā€‹(p.Ile67Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000046 ( 0 hom., cov: 12)
Exomes š‘“: 0.000069 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR2T5
NM_001004697.2 missense

Scores

2
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.450
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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR2T5NM_001004697.2 linkuse as main transcriptc.199A>G p.Ile67Val missense_variant 1/1 ENST00000641363.1
LOC105373277XR_002958498.2 linkuse as main transcriptn.188-3303T>C intron_variant, non_coding_transcript_variant
LOC105373277XR_001738575.2 linkuse as main transcriptn.144-3303T>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.199A>G p.Ile67Val missense_variant 1/1 NM_001004697.2 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
4
AN:
86420
Hom.:
0
Cov.:
12
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000808
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000686
AC:
88
AN:
1283138
Hom.:
0
Cov.:
22
AF XY:
0.0000757
AC XY:
49
AN XY:
647062
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:
0.0000876
Gnomad4 OTH exome
AF:
0.0000743
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000463
AC:
4
AN:
86420
Hom.:
0
Cov.:
12
AF XY:
0.0000243
AC XY:
1
AN XY:
41228
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000808
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000167
AC:
2

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 GeneticsNov 15, 2021The c.199A>G (p.I67V) alteration is located in exon 1 (coding exon 1) of the OR2T5 gene. This alteration results from a A to G substitution at nucleotide position 199, causing the isoleucine (I) at amino acid position 67 to be replaced by a valine (V). 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
0.17
BayesDel_addAF
Benign
-0.43
T
BayesDel_noAF
Benign
-0.69
CADD
Benign
13
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0042
T
Eigen
Benign
-0.23
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.049
N
M_CAP
Benign
0.0012
T
MetaRNN
Uncertain
0.55
D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.2
L
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.33
T
Polyphen
0.87
P
MutPred
0.80
Loss of catalytic residue at L72 (P = 0.2023);
ClinPred
0.13
T
GERP RS
1.2
Varity_R
0.25
gMVP
0.044

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: rs759293827; hg19: chr1-248652088; API