rs202070215

Variant summary

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

The NM_001005324.1(OR10V1):​c.325G>T​(p.Gly109Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G109S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

OR10V1
NM_001005324.1 missense

Scores

1
7
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0990
Variant links:
Genes affected
OR10V1 (HGNC:15136): (olfactory receptor family 10 subfamily V member 1) 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]
STX3 (HGNC:11438): (syntaxin 3) The gene is a member of the syntaxin family. The encoded protein is targeted to the apical membrane of epithelial cells where it forms clusters and is important in establishing and maintaining polarity necessary for protein trafficking involving vesicle fusion and exocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

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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 rank MANE Protein UniProt
OR10V1NM_001005324.1 linkc.325G>T p.Gly109Cys missense_variant Exon 1 of 1 ENST00000307552.3 NP_001005324.1 Q8NGI7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR10V1ENST00000307552.3 linkc.325G>T p.Gly109Cys missense_variant Exon 1 of 1 6 NM_001005324.1 ENSP00000302199.2 Q8NGI7
STX3ENST00000641815 linkc.-510C>A 5_prime_UTR_variant Exon 1 of 12 ENSP00000493027.1 A0A286YF28

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.046
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0048
T
Eigen
Uncertain
0.37
Eigen_PC
Benign
0.18
FATHMM_MKL
Benign
0.21
N
LIST_S2
Uncertain
0.89
D
M_CAP
Benign
0.015
T
MetaRNN
Uncertain
0.45
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.5
M
PrimateAI
Benign
0.33
T
PROVEAN
Pathogenic
-5.6
D
REVEL
Benign
0.22
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.0030
D
Polyphen
1.0
D
Vest4
0.36
MutPred
0.44
Gain of catalytic residue at G109 (P = 0.0351);
MVP
0.80
MPC
0.29
ClinPred
0.99
D
GERP RS
4.4
Varity_R
0.86
gMVP
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-59480994; API