Variant rs35634161 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012351.3(OR10J1):c.176T>C(p.Met59Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0176 in 1,614,140 control chromosomes in the GnomAD database, including 394 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.

Frequency

Genomes: 𝑓 0.015 ( 52 hom., cov: 32)

Exomes 𝑓: 0.018 ( 342 hom. )

Consequence

OR10J1
NM_012351.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.00

Variant links:

Genes affected

OR10J1 (HGNC:8175): (olfactory receptor family 10 subfamily J member 1) 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]

OR10J1 links:

(HGNC:):

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=0.011399478).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.056 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
OR10J1	NM_012351.3 linkuse as main transcript	c.176T>C	p.Met59Thr	missense_variant	1/1	ENST00000423932.6
OR10J1	NM_001363557.2 linkuse as main transcript	c.176T>C	p.Met59Thr	missense_variant	5/5
OR10J1	NM_001363558.2 linkuse as main transcript	c.176T>C	p.Met59Thr	missense_variant	4/4
OR10J1	XM_047417793.1 linkuse as main transcript	c.176T>C	p.Met59Thr	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
OR10J1	ENST00000423932.6 linkuse as main transcript	c.176T>C	p.Met59Thr	missense_variant	1/1		NM_012351.3	P1
	ENST00000431862.1 linkuse as main transcript	n.227+28875A>G		intron_variant, non_coding_transcript_variant		1
OR10J1	ENST00000641630.1 linkuse as main transcript	c.209T>C	p.Met70Thr	missense_variant	1/1
OR10J1	ENST00000642080.1 linkuse as main transcript	c.176T>C	p.Met59Thr	missense_variant	2/2			P1

Frequencies

GnomAD3 genomes

AF:

0.0155

AC:

2352

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00263

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00969

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.0618

Gnomad SAS

AF:

0.00932

Gnomad FIN

AF:

0.0440

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0181

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.0195

AC:

4892

AN:

251148

Hom.:

AF XY:

0.0193

AC XY:

2614

AN XY:

135718

show subpopulations

Gnomad AFR exome

AF:

0.00246

Gnomad AMR exome

AF:

0.00570

Gnomad ASJ exome

AF:

0.00278

Gnomad EAS exome

AF:

0.0578

Gnomad SAS exome

AF:

0.0101

Gnomad FIN exome

AF:

0.0418

Gnomad NFE exome

AF:

0.0197

Gnomad OTH exome

AF:

0.0178

GnomAD4 exome

AF:

0.0178

AC:

26040

AN:

1461844

Hom.:

342

Cov.:

AF XY:

0.0176

AC XY:

12807

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.00233

Gnomad4 AMR exome

AF:

0.00595

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.0765

Gnomad4 SAS exome

AF:

0.0103

Gnomad4 FIN exome

AF:

0.0402

Gnomad4 NFE exome

AF:

0.0167

Gnomad4 OTH exome

AF:

0.0161

GnomAD4 genome

AF:

0.0154

AC:

2351

AN:

152296

Hom.:

Cov.:

AF XY:

0.0163

AC XY:

1216

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00262

Gnomad4 AMR

AF:

0.00967

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.0616

Gnomad4 SAS

AF:

0.00932

Gnomad4 FIN

AF:

0.0440

Gnomad4 NFE

AF:

0.0181

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.0173

Hom.:

Bravo

AF:

0.0126

TwinsUK

AF:

0.0148

AC:

ALSPAC

AF:

0.0182

AC:

ESP6500AA

AF:

0.00386

AC:

ESP6500EA

AF:

0.0187

AC:

161

ExAC

AF:

0.0202

AC:

2452

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.0133

EpiControl

AF:

0.0130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.31

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0064

.;T;.

Eigen

Uncertain

0.68

Eigen_PC

Uncertain

0.53

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.96

.;D;D

MetaRNN

Benign

0.011

T;T;T

MetaSVM

Benign

-0.82

MutationAssessor

Pathogenic

3.4

.;M;.

MutationTaster

Benign

0.025

PrimateAI

Benign

0.23

REVEL

Benign

0.21

Polyphen

1.0

.;D;.

MPC

0.012

ClinPred

0.061

GERP RS

4.5

Varity_R

0.91

gMVP

0.090

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over