11-7825044-A-G

Variant summary

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

The NM_153445.2(OR5P3):ā€‹c.929T>Cā€‹(p.Phe310Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

OR5P3
NM_153445.2 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0940
Variant links:
Genes affected
OR5P3 (HGNC:14784): (olfactory receptor family 5 subfamily P member 3) 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=0.08196941).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OR5P3NM_153445.2 linkc.929T>C p.Phe310Ser missense_variant 2/2 ENST00000641167.1 NP_703146.1 Q8WZ94A0A126GVE6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR5P3ENST00000641167.1 linkc.929T>C p.Phe310Ser missense_variant 2/2 NM_153445.2 ENSP00000492944.1 Q8WZ94
ENSG00000271758ENST00000527565.1 linkn.542+53963T>C intron_variant 3
ENSG00000254951ENST00000529488.5 linkn.531+53963T>C intron_variant 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1459996
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
726372
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

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 GeneticsNov 25, 2024The c.929T>C (p.F310S) alteration is located in exon 1 (coding exon 1) of the OR5P3 gene. This alteration results from a T to C substitution at nucleotide position 929, causing the phenylalanine (F) at amino acid position 310 to be replaced by a serine (S). 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
Benign
0.14
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
15
DANN
Benign
0.91
DEOGEN2
Benign
0.0050
T;T
Eigen
Benign
-0.87
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.10
N
M_CAP
Benign
0.0036
T
MetaRNN
Benign
0.082
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.99
L;L
PrimateAI
Benign
0.30
T
PROVEAN
Uncertain
-2.6
.;D
REVEL
Benign
0.020
Sift
Benign
0.078
.;T
Sift4G
Benign
0.10
.;T
Polyphen
0.36
B;B
Vest4
0.12
MutPred
0.42
Gain of disorder (P = 0.0046);Gain of disorder (P = 0.0046);
MVP
0.31
MPC
0.0095
ClinPred
0.15
T
GERP RS
0.60
Varity_R
0.14
gMVP
0.032

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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: chr11-7846591; API