Variant rs857825 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001005185.2(OR6N1):c.782A>G(p.Gln261Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 1,613,410 control chromosomes in the GnomAD database, including 409,937 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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 0.72 ( 39713 hom., cov: 32)

Exomes 𝑓: 0.71 ( 370224 hom. )

Consequence

OR6N1
NM_001005185.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.81

Variant links:

Genes affected

OR6N1 (HGNC:15034): (olfactory receptor family 6 subfamily N 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]

OR6N1 links:

OR6N1 (HGNC:):

OR6N1 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=1.037083E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6N1	NM_001005185.2 linkuse as main transcript	c.782A>G	p.Gln261Arg	missense_variant	2/2	ENST00000641846.1	NP_001005185.1	Q8NGY5
OR6N1	XM_017000325.2 linkuse as main transcript	c.782A>G	p.Gln261Arg	missense_variant	3/3		XP_016855814.1	Q8NGY5
OR6N1	XM_017000326.2 linkuse as main transcript	c.782A>G	p.Gln261Arg	missense_variant	4/4		XP_016855815.1	Q8NGY5
OR6N1	XM_017000327.2 linkuse as main transcript	c.782A>G	p.Gln261Arg	missense_variant	3/3		XP_016855816.1	Q8NGY5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6N1	ENST00000641846.1 linkuse as main transcript	c.782A>G	p.Gln261Arg	missense_variant	2/2		NM_001005185.2	ENSP00000493254.1		Q8NGY5
OR6N1	ENST00000641189.1 linkuse as main transcript	n.175+6120A>G		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.720

AC:

109494

AN:

151994

Hom.:

39675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.705

Gnomad AMR

AF:

0.756

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.605

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.720

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.708

GnomAD3 exomes

AF:

0.687

AC:

172631

AN:

251342

Hom.:

60650

AF XY:

0.669

AC XY:

90922

AN XY:

135838

show subpopulations

Gnomad AFR exome

AF:

0.781

Gnomad AMR exome

AF:

0.794

Gnomad ASJ exome

AF:

0.659

Gnomad EAS exome

AF:

0.612

Gnomad SAS exome

AF:

0.458

Gnomad FIN exome

AF:

0.730

Gnomad NFE exome

AF:

0.709

Gnomad OTH exome

AF:

0.689

GnomAD4 exome

AF:

0.708

AC:

1034325

AN:

1461298

Hom.:

370224

Cov.:

AF XY:

0.699

AC XY:

508067

AN XY:

726968

show subpopulations

Gnomad4 AFR exome

AF:

0.774

Gnomad4 AMR exome

AF:

0.789

Gnomad4 ASJ exome

AF:

0.656

Gnomad4 EAS exome

AF:

0.619

Gnomad4 SAS exome

AF:

0.460

Gnomad4 FIN exome

AF:

0.726

Gnomad4 NFE exome

AF:

0.726

Gnomad4 OTH exome

AF:

0.700

GnomAD4 genome

AF:

0.720

AC:

109584

AN:

152112

Hom.:

39713

Cov.:

AF XY:

0.713

AC XY:

53008

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.776

Gnomad4 AMR

AF:

0.756

Gnomad4 ASJ

AF:

0.654

Gnomad4 EAS

AF:

0.605

Gnomad4 SAS

AF:

0.436

Gnomad4 FIN

AF:

0.720

Gnomad4 NFE

AF:

0.712

Gnomad4 OTH

AF:

0.710

Alfa

AF:

0.706

Hom.:

84811

Bravo

AF:

0.732

TwinsUK

AF:

0.734

AC:

2721

ALSPAC

AF:

0.729

AC:

2809

ESP6500AA

AF:

0.780

AC:

3436

ESP6500EA

AF:

0.717

AC:

6162

ExAC

AF:

0.679

AC:

82478

Asia WGS

AF:

0.574

AC:

1999

AN:

3478

EpiCase

AF:

0.699

EpiControl

AF:

0.696

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.16

DEOGEN2

Benign

0.0012

T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.92

FATHMM_MKL

Benign

0.028

LIST_S2

Benign

0.032

.;T

MetaRNN

Benign

0.0000010

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-0.75

N;N

PrimateAI

Benign

0.34

PROVEAN

Benign

2.6

.;N

REVEL

Benign

0.093

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

.;T

Polyphen

0.0

B;B

Vest4

0.039

MPC

0.027

ClinPred

0.0040

GERP RS

4.7

Varity_R

0.034

gMVP

0.069

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