Variant rs4925663 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.668G>A(p.Gly223Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 1,613,724 control chromosomes in the GnomAD database, including 128,635 homozygotes. In-silico tool predicts 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 0.36 ( 10382 hom., cov: 31)

Exomes 𝑓: 0.40 ( 118253 hom. )

Consequence

OR2B11
NM_001004492.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.353

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:

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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=6.0917282E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2B11	NM_001004492.2 linkuse as main transcript	c.668G>A	p.Gly223Asp	missense_variant	2/2	ENST00000641149.2
OR2B11	NR_169840.1 linkuse as main transcript	n.1322G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
OR2B11	ENST00000641149.2 linkuse as main transcript	c.668G>A	p.Gly223Asp	missense_variant	2/2	NM_001004492.2	P1
OR2B11	ENST00000641527.1 linkuse as main transcript	c.668G>A	p.Gly223Asp	missense_variant	3/3		P1
OR2B11	ENST00000641613.1 linkuse as main transcript	n.1322G>A		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54251

AN:

151796

Hom.:

10365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.444

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.344

GnomAD3 exomes

AF:

0.406

AC:

101977

AN:

251356

Hom.:

21565

AF XY:

0.406

AC XY:

55167

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.480

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.519

Gnomad SAS exome

AF:

0.446

Gnomad FIN exome

AF:

0.432

Gnomad NFE exome

AF:

0.391

Gnomad OTH exome

AF:

0.392

GnomAD4 exome

AF:

0.398

AC:

582193

AN:

1461810

Hom.:

118253

Cov.:

AF XY:

0.400

AC XY:

290703

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.223

Gnomad4 AMR exome

AF:

0.477

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.445

Gnomad4 FIN exome

AF:

0.436

Gnomad4 NFE exome

AF:

0.398

Gnomad4 OTH exome

AF:

0.374

GnomAD4 genome

AF:

0.357

AC:

54285

AN:

151914

Hom.:

10382

Cov.:

AF XY:

0.362

AC XY:

26900

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.433

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.509

Gnomad4 SAS

AF:

0.464

Gnomad4 FIN

AF:

0.444

Gnomad4 NFE

AF:

0.394

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.383

Hom.:

27818

Bravo

AF:

0.349

TwinsUK

AF:

0.400

AC:

1482

ALSPAC

AF:

0.411

AC:

1583

ESP6500AA

AF:

0.236

AC:

1040

ESP6500EA

AF:

0.390

AC:

3350

ExAC

AF:

0.401

AC:

48726

Asia WGS

AF:

0.478

AC:

1663

AN:

3478

EpiCase

AF:

0.370

EpiControl

AF:

0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.036

T;T;T

Eigen

Benign

-0.12

Eigen_PC

Benign

-0.13

FATHMM_MKL

Benign

0.075

LIST_S2

Benign

0.13

.;.;T

MetaRNN

Benign

0.000061

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.3

M;M;M

MutationTaster

Benign

1.0

PrimateAI

Benign

0.29

PROVEAN

Pathogenic

-4.5

.;.;D

REVEL

Benign

0.13

Sift

Uncertain

0.0030

.;.;D

Sift4G

Uncertain

0.055

.;.;T

Polyphen

0.35

B;B;B

Vest4

0.18

MPC

0.30

ClinPred

0.068

GERP RS

4.2

Varity_R

0.82

gMVP

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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