rs372285751

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_153444.1(OR5P2):​c.532G>T​(p.Ala178Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,456,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. A178P) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR5P2
NM_153444.1 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97
Variant links:
Genes affected
OR5P2 (HGNC:14783): (olfactory receptor family 5 subfamily P member 2) 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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04064721).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR5P2NM_153444.1 linkc.532G>T p.Ala178Ser missense_variant Exon 1 of 1 ENST00000329434.3 NP_703145.1 Q8WZ92A0A126GVJ7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR5P2ENST00000329434.3 linkc.532G>T p.Ala178Ser missense_variant Exon 1 of 1 6 NM_153444.1 ENSP00000331823.2 Q8WZ92
ENSG00000271758ENST00000527565.1 linkn.542+82596G>T intron_variant Intron 5 of 5 3
ENSG00000254951ENST00000529488.5 linkn.532-41890G>T intron_variant Intron 5 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
147206
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1456408
Hom.:
0
Cov.:
34
AF XY:
0.00
AC XY:
0
AN XY:
724660
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000509
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
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
147206
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
71810
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
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
Benign
0.088
BayesDel_addAF
Benign
-0.36
T
BayesDel_noAF
Benign
-0.76
CADD
Benign
6.3
DANN
Benign
0.56
DEOGEN2
Benign
0.00079
T
Eigen
Benign
-0.98
Eigen_PC
Benign
-0.90
FATHMM_MKL
Benign
0.19
N
M_CAP
Benign
0.0044
T
MetaRNN
Benign
0.041
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.72
N
PrimateAI
Benign
0.19
T
PROVEAN
Benign
0.84
N
REVEL
Benign
0.032
Sift
Benign
0.91
T
Sift4G
Benign
0.33
T
Polyphen
0.055
B
Vest4
0.044
MutPred
0.44
Loss of catalytic residue at A178 (P = 0.0291);
MVP
0.085
MPC
0.0069
ClinPred
0.15
T
GERP RS
1.2
Varity_R
0.052
gMVP
0.086

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: chr11-7817958; API