Genetic Variant OR5P2:p.Arg27Gln (chr11-7796863-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_153444.1(OR5P2):c.80G>A(p.Arg27Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 1,225,246 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0014 ( 10 hom., cov: 30)

Exomes 𝑓: 0.0022 ( 73 hom. )

Consequence

OR5P2
NM_153444.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.347

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]

OR5P2 links:

ENSG00000271758 (HGNC:):

ENSG00000271758 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.012401998).

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR5P2	NM_153444.1 link	c.80G>A	p.Arg27Gln	missense_variant	Exon 1 of 1	ENST00000329434.3	NP_703145.1	Q8WZ92A0A126GVJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
OR5P2	ENST00000329434.3 link	c.80G>A	p.Arg27Gln	missense_variant	Exon 1 of 1	6	NM_153444.1	ENSP00000331823.2	Q8WZ92
ENSG00000271758	ENST00000527565.1 link	n.542+82144G>A		intron_variant	Intron 5 of 5	3
ENSG00000254951	ENST00000529488.5 link	n.532-42342G>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.00137

AC:

164

AN:

119502

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000767

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000741

Gnomad ASJ

AF:

0.00170

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000360

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00220

Gnomad OTH

AF:

0.00120

GnomAD3 exomes

AF:

0.00111

AC:

211

AN:

190388

Hom.:

AF XY:

0.00108

AC XY:

112

AN XY:

103756

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.000426

Gnomad ASJ exome

AF:

0.00188

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000417

Gnomad NFE exome

AF:

0.00198

Gnomad OTH exome

AF:

0.000670

GnomAD4 exome

AF:

0.00215

AC:

2382

AN:

1105744

Hom.:

Cov.:

AF XY:

0.00207

AC XY:

1143

AN XY:

551552

show subpopulations

Gnomad4 AFR exome

AF:

0.000133

Gnomad4 AMR exome

AF:

0.000512

Gnomad4 ASJ exome

AF:

0.00178

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000142

Gnomad4 FIN exome

AF:

0.000495

Gnomad4 NFE exome

AF:

0.00269

Gnomad4 OTH exome

AF:

0.00141

GnomAD4 genome

AF:

0.00137

AC:

164

AN:

119502

Hom.:

Cov.:

AF XY:

0.00117

AC XY:

AN XY:

58316

show subpopulations

Gnomad4 AFR

AF:

0.000767

Gnomad4 AMR

AF:

0.000741

Gnomad4 ASJ

AF:

0.00170

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000360

Gnomad4 NFE

AF:

0.00220

Gnomad4 OTH

AF:

0.00120

Alfa

AF:

0.00158

Hom.:

Bravo

AF:

0.00120

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.00119

AC:

ESP6500EA

AF:

0.00186

AC:

ExAC

AF:

0.000730

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Jan 23, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.80G>A (p.R27Q) alteration is located in exon 1 (coding exon 1) of the OR5P2 gene. This alteration results from a G to A substitution at nucleotide position 80, causing the arginine (R) at amino acid position 27 to be replaced by a glutamine (Q). 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

0.093

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.72

CADD

Benign

6.8

DANN

Benign

0.67

DEOGEN2

Benign

0.0023

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.038

M_CAP

Benign

0.011

MetaRNN

Benign

0.012

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.0

PrimateAI

Benign

0.18

PROVEAN

Benign

-0.87

REVEL

Benign

0.084

Sift

Benign

0.76

Sift4G

Benign

1.0

Polyphen

0.024

Vest4

0.049

MVP

0.17

MPC

0.0054

ClinPred

0.0015

GERP RS

-0.33

Varity_R

0.041

gMVP

0.26

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over