Variant chr5-181155604-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_206880.2(OR2V2):c.662A>G(p.His221Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,613,848 control chromosomes in the GnomAD database, including 261,758 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.63 ( 30769 hom., cov: 32)

Exomes 𝑓: 0.56 ( 230989 hom. )

Consequence

OR2V2
NM_206880.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.29

Variant links:

Genes affected

OR2V2 (HGNC:15341): (olfactory receptor family 2 subfamily V 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]

OR2V2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.705043E-7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2V2	NM_206880.2 linkuse as main transcript	c.662A>G	p.His221Arg	missense_variant	2/2	ENST00000641492.1	NP_996763.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2V2	ENST00000641492.1 linkuse as main transcript	c.662A>G	p.His221Arg	missense_variant	2/2		NM_206880.2	ENSP00000493207	P1
OR2V2	ENST00000641791.1 linkuse as main transcript	c.662A>G	p.His221Arg	missense_variant	3/3			ENSP00000493017	P1

Frequencies

GnomAD3 genomes

AF:

0.627

AC:

95255

AN:

151906

Hom.:

30719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.782

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.696

Gnomad ASJ

AF:

0.518

Gnomad EAS

AF:

0.569

Gnomad SAS

AF:

0.613

Gnomad FIN

AF:

0.560

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.540

Gnomad OTH

AF:

0.634

GnomAD3 exomes

AF:

0.598

AC:

150289

AN:

251482

Hom.:

46274

AF XY:

0.591

AC XY:

80361

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.787

Gnomad AMR exome

AF:

0.761

Gnomad ASJ exome

AF:

0.526

Gnomad EAS exome

AF:

0.554

Gnomad SAS exome

AF:

0.636

Gnomad FIN exome

AF:

0.552

Gnomad NFE exome

AF:

0.533

Gnomad OTH exome

AF:

0.585

GnomAD4 exome

AF:

0.559

AC:

816673

AN:

1461824

Hom.:

230989

Cov.:

AF XY:

0.560

AC XY:

407276

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.797

Gnomad4 AMR exome

AF:

0.751

Gnomad4 ASJ exome

AF:

0.531

Gnomad4 EAS exome

AF:

0.594

Gnomad4 SAS exome

AF:

0.638

Gnomad4 FIN exome

AF:

0.547

Gnomad4 NFE exome

AF:

0.537

Gnomad4 OTH exome

AF:

0.566

GnomAD4 genome

AF:

0.627

AC:

95372

AN:

152024

Hom.:

30769

Cov.:

AF XY:

0.631

AC XY:

46843

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.782

Gnomad4 AMR

AF:

0.696

Gnomad4 ASJ

AF:

0.518

Gnomad4 EAS

AF:

0.569

Gnomad4 SAS

AF:

0.614

Gnomad4 FIN

AF:

0.560

Gnomad4 NFE

AF:

0.540

Gnomad4 OTH

AF:

0.638

Alfa

AF:

0.556

Hom.:

57918

Bravo

AF:

0.645

TwinsUK

AF:

0.540

AC:

2004

ALSPAC

AF:

0.550

AC:

2120

ESP6500AA

AF:

0.779

AC:

3431

ESP6500EA

AF:

0.533

AC:

4588

ExAC

AF:

0.592

AC:

71890

Asia WGS

AF:

0.639

AC:

2223

AN:

3478

EpiCase

AF:

0.542

EpiControl

AF:

0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.89

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.047

DANN

Benign

0.087

DEOGEN2

Benign

0.0031

T;T;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0028

LIST_S2

Benign

0.034

.;.;T

MetaRNN

Benign

8.7e-7

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.35

N;N;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.17

PROVEAN

Benign

1.7

.;.;N

REVEL

Benign

0.0090

Sift

Benign

1.0

.;.;T

Sift4G

Benign

0.54

.;.;T

Polyphen

0.0

B;B;B

Vest4

0.0030

MPC

0.086

ClinPred

0.0020

GERP RS

0.49

Varity_R

0.038

gMVP

0.12

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over