9-122750491-T-G

Variant summary

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

The NM_001004453.3(OR1L6):ā€‹c.644T>Gā€‹(p.Ile215Ser) variant causes a missense change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000075 ( 0 hom., cov: 16)
Exomes š‘“: 0.0000035 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR1L6
NM_001004453.3 missense

Scores

4
6
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.83
Variant links:
Genes affected
OR1L6 (HGNC:8218): (olfactory receptor family 1 subfamily L member 6) 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 Protein UniProt
OR1L6NM_001004453.3 linkc.644T>G p.Ile215Ser missense_variant 2/2 ENST00000304720.3 NP_001004453.2 Q8NGR2A0A0C4DFP2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR1L6ENST00000304720.3 linkc.644T>G p.Ile215Ser missense_variant 2/26 NM_001004453.3 ENSP00000304235.2 A0A0C4DFP2
OR1L6ENST00000373684.1 linkc.752T>G p.Ile251Ser missense_variant 1/16 ENSP00000362788.1 Q8NGR2

Frequencies

GnomAD3 genomes
AF:
0.00000754
AC:
1
AN:
132690
Hom.:
0
Cov.:
16
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000800
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000105
AC:
2
AN:
190408
Hom.:
0
AF XY:
0.0000197
AC XY:
2
AN XY:
101368
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000674
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:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000350
AC:
3
AN:
856498
Hom.:
0
Cov.:
12
AF XY:
0.00000450
AC XY:
2
AN XY:
444366
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000723
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000754
AC:
1
AN:
132690
Hom.:
0
Cov.:
16
AF XY:
0.00
AC XY:
0
AN XY:
63178
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000800
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.46
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.22
CADD
Pathogenic
27
DANN
Uncertain
0.99
DEOGEN2
Benign
0.036
.;T
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.69
T;T
M_CAP
Benign
0.0029
T
MetaRNN
Uncertain
0.73
D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Pathogenic
3.7
.;H
PrimateAI
Benign
0.27
T
PROVEAN
Pathogenic
-5.8
D;D
REVEL
Benign
0.15
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.99
.;D
Vest4
0.62
MutPred
0.58
.;Loss of stability (P = 0.0236);
MVP
0.88
MPC
0.93
ClinPred
0.93
D
GERP RS
3.4
Varity_R
0.87
gMVP
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs10985760; hg19: chr9-125512770; API