Variant chr6-27911422-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_033057.2(OR2B2):c.898G>T(p.Ala300Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 1,613,772 control chromosomes in the GnomAD database, including 7,111 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 0.053 ( 327 hom., cov: 32)

Exomes 𝑓: 0.086 ( 6784 hom. )

Consequence

OR2B2
NM_033057.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Variant links:

Genes affected

OR2B2 (HGNC:13966): (olfactory receptor family 2 subfamily B 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]

OR2B2 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=0.0019125342).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2B2	NM_033057.2 linkuse as main transcript	c.898G>T	p.Ala300Ser	missense_variant	1/1	ENST00000303324.4	NP_149046.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2B2	ENST00000303324.4 linkuse as main transcript	c.898G>T	p.Ala300Ser	missense_variant	1/1		NM_033057.2	ENSP00000304419	P1

Frequencies

GnomAD3 genomes

AF:

0.0533

AC:

8112

AN:

152110

Hom.:

327

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0257

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0259

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.0398

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0874

Gnomad OTH

AF:

0.0397

GnomAD3 exomes

AF:

0.0477

AC:

11992

AN:

251214

Hom.:

483

AF XY:

0.0474

AC XY:

6433

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.0280

Gnomad AMR exome

AF:

0.0202

Gnomad ASJ exome

AF:

0.0227

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000523

Gnomad FIN exome

AF:

0.0392

Gnomad NFE exome

AF:

0.0833

Gnomad OTH exome

AF:

0.0462

GnomAD4 exome

AF:

0.0860

AC:

125740

AN:

1461544

Hom.:

6784

Cov.:

AF XY:

0.0826

AC XY:

60082

AN XY:

727098

show subpopulations

Gnomad4 AFR exome

AF:

0.0240

Gnomad4 AMR exome

AF:

0.0203

Gnomad4 ASJ exome

AF:

0.0241

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.000557

Gnomad4 FIN exome

AF:

0.0404

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.0697

GnomAD4 genome

AF:

0.0533

AC:

8112

AN:

152228

Hom.:

327

Cov.:

AF XY:

0.0483

AC XY:

3596

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0258

Gnomad4 AMR

AF:

0.0258

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.0398

Gnomad4 NFE

AF:

0.0874

Gnomad4 OTH

AF:

0.0393

Alfa

AF:

0.0787

Hom.:

735

Bravo

AF:

0.0515

TwinsUK

AF:

0.125

AC:

462

ALSPAC

AF:

0.111

AC:

426

ESP6500AA

AF:

0.0361

AC:

159

ESP6500EA

AF:

0.0876

AC:

753

ExAC

AF:

0.0482

AC:

5850

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.56

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0067

Eigen

Benign

-0.013

Eigen_PC

Benign

-0.064

FATHMM_MKL

Benign

0.21

LIST_S2

Benign

0.85

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.0

MutationTaster

Benign

1.0

PrimateAI

Benign

0.23

PROVEAN

Uncertain

-2.8

REVEL

Benign

0.073

Sift

Uncertain

0.0060

Sift4G

Uncertain

0.010

Polyphen

0.97

Vest4

0.084

MPC

0.20

ClinPred

0.034

GERP RS

3.6

Varity_R

0.30

gMVP

0.13

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