rs775730015

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001005160.3(OR52A5):​c.562G>T​(p.Val188Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 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. V188M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

OR52A5
NM_001005160.3 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.791
Variant links:
Genes affected
OR52A5 (HGNC:19580): (olfactory receptor family 52 subfamily A 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.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21311358).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR52A5NM_001005160.3 linkc.562G>T p.Val188Leu missense_variant Exon 2 of 2 ENST00000307388.2 NP_001005160.1 Q9H2C5A0A126GWD2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR52A5ENST00000307388.2 linkc.562G>T p.Val188Leu missense_variant Exon 2 of 2 6 NM_001005160.3 ENSP00000303469.1 Q9H2C5
OR52A5ENST00000642125.1 linkc.562G>T p.Val188Leu missense_variant Exon 2 of 2 ENSP00000493298.1 Q9H2C5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
18
DANN
Uncertain
0.99
DEOGEN2
Benign
0.012
T;T
Eigen
Benign
-0.13
Eigen_PC
Benign
-0.14
FATHMM_MKL
Benign
0.20
N
LIST_S2
Uncertain
0.86
.;D
M_CAP
Benign
0.0063
T
MetaRNN
Benign
0.21
T;T
MetaSVM
Uncertain
-0.22
T
MutationAssessor
Benign
1.6
L;L
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-1.5
.;N
REVEL
Benign
0.11
Sift
Benign
0.19
.;T
Sift4G
Benign
0.11
.;T
Polyphen
0.56
P;P
Vest4
0.046
MutPred
0.46
Loss of methylation at K189 (P = 0.0358);Loss of methylation at K189 (P = 0.0358);
MVP
0.24
MPC
0.022
ClinPred
0.76
D
GERP RS
4.2
Varity_R
0.15
gMVP
0.084

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: rs775730015; hg19: chr11-5153311; API