Genetic Variant NM_153444.1:c.80G>A (chr11-7796863-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -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. 16/22 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

Publications

4 publications found

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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

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

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153444.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5P2	NM_153444.1	MANE Select	c.80G>A	p.Arg27Gln	missense	Exon 1 of 1	NP_703145.1	A0A126GVJ7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR5P2	ENST00000329434.3	TSL:6 MANE Select	c.80G>A	p.Arg27Gln	missense	Exon 1 of 1	ENSP00000331823.2	Q8WZ92
ENSG00000271758	ENST00000527565.1	TSL:3	n.542+82144G>A		intron	N/A
ENSG00000254951	ENST00000529488.5	TSL:5	n.532-42342G>A		intron	N/A

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

GnomAD2 exomes

AF:

0.00111

AC:

211

AN:

190388

AF XY:

0.00108

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 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

African (AFR)

AF:

0.000133

AC:

AN:

22604

American (AMR)

AF:

0.000512

AC:

AN:

31256

Ashkenazi Jewish (ASJ)

AF:

0.00178

AC:

AN:

20822

East Asian (EAS)

AF:

0.00

AC:

AN:

35484

South Asian (SAS)

AF:

0.0000142

AC:

AN:

70426

European-Finnish (FIN)

AF:

0.000495

AC:

AN:

42460

Middle Eastern (MID)

AF:

0.000411

AC:

AN:

4864

European-Non Finnish (NFE)

AF:

0.00269

AC:

2236

AN:

831184

Other (OTH)

AF:

0.00141

AC:

AN:

46644

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

107

214

322

429

536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00137

AC:

164

AN:

119502

Hom.:

Cov.:

AF XY:

0.00117

AC XY:

AN XY:

58316

show subpopulations

African (AFR)

AF:

0.000767

AC:

AN:

28676

American (AMR)

AF:

0.000741

AC:

AN:

12144

Ashkenazi Jewish (ASJ)

AF:

0.00170

AC:

AN:

2940

East Asian (EAS)

AF:

0.00

AC:

AN:

4626

South Asian (SAS)

AF:

0.00

AC:

AN:

4220

European-Finnish (FIN)

AF:

0.000360

AC:

AN:

8342

Middle Eastern (MID)

AF:

0.00

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.00220

AC:

123

AN:

55828

Other (OTH)

AF:

0.00120

AC:

AN:

1664

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.72

CADD

Benign

6.8

(source)

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

PhyloP100

-0.35

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

PromoterAI

-0.026

Neutral

(source)

Varity_R

0.041

gMVP

0.26

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over