Variant 2-240030066-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001005853.1(OR6B2):c.364C>T(p.Arg122Cys) variant causes a missense change. The variant allele was found at a frequency of 0.296 in 1,414,392 control chromosomes in the GnomAD database, including 52,973 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6413 hom., cov: 29)

Exomes 𝑓: 0.30 ( 46560 hom. )

Consequence

OR6B2
NM_001005853.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 5.22

Variant links:

Genes affected

OR6B2 (HGNC:15041): (olfactory receptor family 6 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]

OR6B2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002757579).

BP6

Variant 2-240030066-G-A is Benign according to our data. Variant chr2-240030066-G-A is described in ClinVar as [Benign]. Clinvar id is 769269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6B2	NM_001005853.1 linkuse as main transcript	c.364C>T	p.Arg122Cys	missense_variant	1/1	ENST00000319423.5	NP_001005853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6B2	ENST00000319423.5 linkuse as main transcript	c.364C>T	p.Arg122Cys	missense_variant	1/1		NM_001005853.1	ENSP00000322435	P1

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41244

AN:

150554

Hom.:

6412

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.268

GnomAD3 exomes

AF:

0.292

AC:

59225

AN:

202930

Hom.:

7681

AF XY:

0.288

AC XY:

31813

AN XY:

110450

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.290

Gnomad ASJ exome

AF:

0.267

Gnomad EAS exome

AF:

0.400

Gnomad SAS exome

AF:

0.173

Gnomad FIN exome

AF:

0.417

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.299

AC:

377752

AN:

1263720

Hom.:

46560

Cov.:

AF XY:

0.297

AC XY:

188595

AN XY:

635678

show subpopulations

Gnomad4 AFR exome

AF:

0.0988

Gnomad4 AMR exome

AF:

0.288

Gnomad4 ASJ exome

AF:

0.269

Gnomad4 EAS exome

AF:

0.382

Gnomad4 SAS exome

AF:

0.180

Gnomad4 FIN exome

AF:

0.427

Gnomad4 NFE exome

AF:

0.307

Gnomad4 OTH exome

AF:

0.296

GnomAD4 genome

AF:

0.274

AC:

41248

AN:

150672

Hom.:

6413

Cov.:

AF XY:

0.277

AC XY:

20365

AN XY:

73548

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.419

Gnomad4 SAS

AF:

0.187

Gnomad4 FIN

AF:

0.437

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.249

Hom.:

1054

Bravo

AF:

0.261

ExAC

AF:

0.263

AC:

31072

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 27, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.15

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.099

Eigen

Uncertain

0.48

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.84

MetaRNN

Benign

0.0028

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.8

MutationTaster

Benign

0.000027

PrimateAI

Benign

0.28

PROVEAN

Pathogenic

-6.8

REVEL

Uncertain

0.61

Sift

Uncertain

0.010

Sift4G

Pathogenic

0.0

Polyphen

0.99

Vest4

0.27

MPC

1.2

ClinPred

0.057

GERP RS

3.5

Varity_R

0.45

gMVP

0.79

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over