Variant 6-29112227-A-G 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.337A>G(p.Thr113Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,613,856 control chromosomes in the GnomAD database, including 15,213 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 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 0.18 ( 3266 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11947 hom. )

Consequence

OR2J3
NM_001005216.4 missense

Scores

Clinical Significance

Affects no assertion criteria provided O:1

Conservation

PhyloP100: 0.633

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:

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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=0.0047168434).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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.337A>G	p.Thr113Ala	missense_variant	4/4	ENST00000641151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
OR2J3	ENST00000641151.2 linkuse as main transcript	c.337A>G	p.Thr113Ala	missense_variant	4/4	NM_001005216.4	P1
OR2J3	ENST00000377169.2 linkuse as main transcript	c.337A>G	p.Thr113Ala	missense_variant	1/1		P1
OR2J3	ENST00000641960.1 linkuse as main transcript	c.337A>G	p.Thr113Ala	missense_variant	5/5		P1

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27203

AN:

151992

Hom.:

3258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.178

GnomAD3 exomes

AF:

0.142

AC:

35484

AN:

249358

Hom.:

3088

AF XY:

0.138

AC XY:

18647

AN XY:

135316

show subpopulations

Gnomad AFR exome

AF:

0.349

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.114

Gnomad SAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.114

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.119

AC:

174437

AN:

1461746

Hom.:

11947

Cov.:

AF XY:

0.120

AC XY:

87069

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.356

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.166

Gnomad4 EAS exome

AF:

0.110

Gnomad4 SAS exome

AF:

0.136

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.108

Gnomad4 OTH exome

AF:

0.125

GnomAD4 genome

AF:

0.179

AC:

27253

AN:

152110

Hom.:

3266

Cov.:

AF XY:

0.178

AC XY:

13205

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.341

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.105

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.144

Hom.:

924

Bravo

AF:

0.195

TwinsUK

AF:

0.108

AC:

401

ALSPAC

AF:

0.108

AC:

417

ESP6500AA

AF:

0.297

AC:

809

ESP6500EA

AF:

0.108

AC:

569

ExAC

AF:

0.144

AC:

17479

EpiCase

AF:

0.107

EpiControl

AF:

0.116

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

0.080

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.96

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.028

LIST_S2

Benign

0.090

.;.;T

MetaRNN

Benign

0.0047

T;T;T

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

PrimateAI

Benign

0.25

PROVEAN

Uncertain

-3.7

.;.;D

REVEL

Benign

0.019

Sift

Benign

0.078

.;.;T

Sift4G

Benign

0.093

.;.;T

Vest4

0.043

MPC

0.13

ClinPred

0.0062

GERP RS

2.8

gMVP

0.11

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