Variant rs12065526 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001004492.2(OR2B11):c.878C>T(p.Thr293Ile) variant causes a missense change. The variant allele was found at a frequency of 0.136 in 1,512,254 control chromosomes in the GnomAD database, including 15,196 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 0.15 ( 1965 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13231 hom. )

Consequence

OR2B11
NM_001004492.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.67

Variant links:

Genes affected

OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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]

OR2B11 links:

OR2B11 (HGNC:):

OR2B11 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=9.048879E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2B11	NM_001004492.2 linkuse as main transcript	c.878C>T	p.Thr293Ile	missense_variant	2/2	ENST00000641149.2	NP_001004492.1	Q5JQS5A0A126GVY5
OR2B11	NR_169840.1 linkuse as main transcript	n.1532C>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2B11	ENST00000641149.2 linkuse as main transcript	c.878C>T	p.Thr293Ile	missense_variant	2/2	NM_001004492.2	ENSP00000492892.1	Q5JQS5
OR2B11	ENST00000641527.1 linkuse as main transcript	c.878C>T	p.Thr293Ile	missense_variant	3/3		ENSP00000493421.1	Q5JQS5
OR2B11	ENST00000641613.1 linkuse as main transcript	n.1532C>T		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23211

AN:

151986

Hom.:

1958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.168

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.0584

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.163

GnomAD3 exomes

AF:

0.128

AC:

23036

AN:

179832

Hom.:

1769

AF XY:

0.127

AC XY:

11966

AN XY:

94236

show subpopulations

Gnomad AFR exome

AF:

0.202

Gnomad AMR exome

AF:

0.154

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.00144

Gnomad SAS exome

AF:

0.0629

Gnomad FIN exome

AF:

0.128

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.125

GnomAD4 exome

AF:

0.134

AC:

182727

AN:

1360150

Hom.:

13231

Cov.:

AF XY:

0.132

AC XY:

88023

AN XY:

665800

show subpopulations

Gnomad4 AFR exome

AF:

0.203

Gnomad4 AMR exome

AF:

0.158

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.00239

Gnomad4 SAS exome

AF:

0.0648

Gnomad4 FIN exome

AF:

0.122

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.153

AC:

23244

AN:

152104

Hom.:

1965

Cov.:

AF XY:

0.148

AC XY:

11041

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.182

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.0591

Gnomad4 FIN

AF:

0.124

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.161

Alfa

AF:

0.143

Hom.:

3795

Bravo

AF:

0.160

TwinsUK

AF:

0.133

AC:

493

ALSPAC

AF:

0.134

AC:

515

ESP6500AA

AF:

0.200

AC:

880

ESP6500EA

AF:

0.145

AC:

1249

ExAC

AF:

0.123

AC:

14413

Asia WGS

AF:

0.0510

AC:

179

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.047

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

8.8

DANN

Benign

0.62

DEOGEN2

Benign

0.0011

T;T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.0082

LIST_S2

Benign

0.48

.;.;T

MetaRNN

Benign

0.00090

T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-3.8

N;N;N

PrimateAI

Benign

0.26

PROVEAN

Benign

4.7

.;.;N

REVEL

Benign

0.12

Sift

Benign

1.0

.;.;T

Sift4G

Benign

1.0

.;.;T

Polyphen

0.0

B;B;B

Vest4

0.058

MPC

0.091

ClinPred

0.0036

GERP RS

5.1

Varity_R

0.046

gMVP

0.075

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

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