Variant chr6-29112567-G-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_001005216.4(OR2J3):c.677G>A(p.Arg226Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,613,344 control chromosomes in the GnomAD database, including 60,389 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Affects (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.34 ( 10281 hom., cov: 32)

Exomes 𝑓: 0.25 ( 50108 hom. )

Consequence

OR2J3
NM_001005216.4 missense

Scores

Clinical Significance

Affects no assertion criteria provided O:1

Conservation

PhyloP100: -1.66

Variant links:

Genes affected

OR2J3 (HGNC:8261): (olfactory receptor family 2 subfamily J member 3) This gene encodes a G-protein-coupled receptor (GPCR) that functions as an olfactory receptor. Olfactory receptors interact with odorant molecules in the nose to initiate a neuronal response that triggers the perception of a smell. The protein encoded by this gene responds to cis-3-hexen-1-ol, which is released by wounded plants, including cut grass. This gene is situated in a cluster of similar olfactory-receptor coding genes on chromosome 6. [provided by RefSeq, May 2013]

OR2J3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.120634E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2J3	NM_001005216.4 linkuse as main transcript	c.677G>A	p.Arg226Gln	missense_variant	4/4	ENST00000641151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
OR2J3	ENST00000641151.2 linkuse as main transcript	c.677G>A	p.Arg226Gln	missense_variant	4/4	NM_001005216.4	P1
OR2J3	ENST00000377169.2 linkuse as main transcript	c.677G>A	p.Arg226Gln	missense_variant	1/1		P1
OR2J3	ENST00000641960.1 linkuse as main transcript	c.677G>A	p.Arg226Gln	missense_variant	5/5		P1

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51399

AN:

151770

Hom.:

10258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.362

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.339

GnomAD3 exomes

AF:

0.293

AC:

72761

AN:

248488

Hom.:

11800

AF XY:

0.294

AC XY:

39611

AN XY:

134946

show subpopulations

Gnomad AFR exome

AF:

0.560

Gnomad AMR exome

AF:

0.282

Gnomad ASJ exome

AF:

0.395

Gnomad EAS exome

AF:

0.231

Gnomad SAS exome

AF:

0.376

Gnomad FIN exome

AF:

0.288

Gnomad NFE exome

AF:

0.240

Gnomad OTH exome

AF:

0.279

GnomAD4 exome

AF:

0.251

AC:

366660

AN:

1461452

Hom.:

50108

Cov.:

AF XY:

0.255

AC XY:

185712

AN XY:

727016

show subpopulations

Gnomad4 AFR exome

AF:

0.569

Gnomad4 AMR exome

AF:

0.284

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.201

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.287

Gnomad4 NFE exome

AF:

0.226

Gnomad4 OTH exome

AF:

0.274

GnomAD4 genome

AF:

0.339

AC:

51463

AN:

151892

Hom.:

10281

Cov.:

AF XY:

0.341

AC XY:

25327

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.554

Gnomad4 AMR

AF:

0.290

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.226

Gnomad4 SAS

AF:

0.361

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.235

Gnomad4 OTH

AF:

0.336

Alfa

AF:

0.263

Hom.:

10147

Bravo

AF:

0.351

TwinsUK

AF:

0.222

AC:

824

ALSPAC

AF:

0.229

AC:

881

ESP6500AA

AF:

0.516

AC:

1332

ESP6500EA

AF:

0.232

AC:

1194

ExAC

AF:

0.297

AC:

35799

Asia WGS

AF:

0.296

AC:

1034

AN:

3478

EpiCase

AF:

0.238

EpiControl

AF:

0.246

ClinVar

Significance: Affects

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

C3HEX, ability to smell

Other:1

Affects, no assertion criteria provided

literature only

OMIM

Sep 01, 2012

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

2.7

DANN

Benign

0.56

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.32

.;.;T

MetaRNN

Benign

0.000071

T;T;T

MetaSVM

Benign

-0.99

MutationTaster

Benign

1.0

PrimateAI

Benign

0.19

PROVEAN

Benign

-0.60

.;.;N

REVEL

Benign

0.0070

Sift

Benign

0.56

.;.;T

Sift4G

Benign

0.73

.;.;T

Vest4

0.0070

MPC

0.13

ClinPred

0.000019

GERP RS

-4.1

gMVP

0.10

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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