11-59477929-C-T

Variant summary

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

The NM_001004705.2(OR4D10):​c.500C>T​(p.Pro167Leu) 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. P167R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)

Consequence

OR4D10
NM_001004705.2 missense

Scores

4
4
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48
Variant links:
Genes affected
OR4D10 (HGNC:15173): (olfactory receptor family 4 subfamily D member 10) 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]

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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
OR4D10NM_001004705.2 linkc.500C>T p.Pro167Leu missense_variant Exon 3 of 3 ENST00000530162.2 NP_001004705.1 Q8NGI6A0A126GVJ1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR4D10ENST00000530162.2 linkc.500C>T p.Pro167Leu missense_variant Exon 3 of 3 6 NM_001004705.2 ENSP00000436424.1 Q8NGI6

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.11
T
Eigen
Uncertain
0.31
Eigen_PC
Benign
0.12
FATHMM_MKL
Benign
0.48
N
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.49
T
MetaSVM
Benign
-0.30
T
MutationAssessor
Pathogenic
3.2
M
PrimateAI
Benign
0.29
T
PROVEAN
Pathogenic
-9.8
D
REVEL
Benign
0.15
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.23
MutPred
0.52
Gain of sheet (P = 0.1208);
MVP
0.75
MPC
0.12
ClinPred
1.0
D
GERP RS
4.7
Varity_R
0.55
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: chr11-59245402; API