11-124023178-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001001953.1(OR10G9):​c.166C>A​(p.Pro56Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000185 in 1,461,500 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

OR10G9
NM_001001953.1 missense

Scores

3
7
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.43
Variant links:
Genes affected
OR10G9 (HGNC:15129): (olfactory receptor family 10 subfamily G member 9) 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 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR10G9NM_001001953.1 linkuse as main transcriptc.166C>A p.Pro56Thr missense_variant 1/1 ENST00000375024.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR10G9ENST00000375024.1 linkuse as main transcriptc.166C>A p.Pro56Thr missense_variant 1/1 NM_001001953.1 P1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD3 exomes
AF:
0.0000480
AC:
12
AN:
250224
Hom.:
0
AF XY:
0.0000296
AC XY:
4
AN XY:
135188
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000868
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000218
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000355
Gnomad OTH exome
AF:
0.000164
GnomAD4 exome
AF:
0.0000185
AC:
27
AN:
1461500
Hom.:
0
Cov.:
36
AF XY:
0.0000165
AC XY:
12
AN XY:
727056
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000227
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000810
Gnomad4 OTH exome
AF:
0.0000331
GnomAD4 genome
Cov.:
29
ExAC
AF:
0.0000330
AC:
4

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 01, 2024The c.166C>A (p.P56T) alteration is located in exon 1 (coding exon 1) of the OR10G9 gene. This alteration results from a C to A substitution at nucleotide position 166, causing the proline (P) at amino acid position 56 to be replaced by a threonine (T). 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
Uncertain
0.52
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.013
T
Eigen
Uncertain
0.23
Eigen_PC
Uncertain
0.23
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.71
T
M_CAP
Benign
0.0021
T
MetaRNN
Uncertain
0.69
D
MetaSVM
Benign
-1.1
T
MutationAssessor
Pathogenic
4.3
H
MutationTaster
Benign
1.0
D
PrimateAI
Benign
0.27
T
PROVEAN
Pathogenic
-7.0
D
REVEL
Benign
0.28
Sift
Uncertain
0.0040
D
Sift4G
Uncertain
0.0070
D
Polyphen
0.035
B
Vest4
0.76
MVP
0.52
MPC
0.37
ClinPred
0.39
T
GERP RS
3.3
Varity_R
0.79
gMVP
0.14

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: rs756703887; hg19: chr11-123893885; API