Variant chr1-158766655-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001005185.2(OR6N1):c.28G>A(p.Ala10Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 1,610,542 control chromosomes in the GnomAD database, including 79,110 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 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 0.25 ( 5867 hom., cov: 31)

Exomes 𝑓: 0.31 ( 73243 hom. )

Consequence

OR6N1
NM_001005185.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
OR6N1	NM_001005185.2 linkuse as main transcript	c.28G>A	p.Ala10Thr	missense_variant	2/2	ENST00000641846.1
OR6N1	XM_017000325.2 linkuse as main transcript	c.28G>A	p.Ala10Thr	missense_variant	3/3
OR6N1	XM_017000326.2 linkuse as main transcript	c.28G>A	p.Ala10Thr	missense_variant	4/4
OR6N1	XM_017000327.2 linkuse as main transcript	c.28G>A	p.Ala10Thr	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR6N1	ENST00000641846.1 linkuse as main transcript	c.28G>A	p.Ala10Thr	missense_variant	2/2		NM_001005185.2	P1
OR6N1	ENST00000641189.1 linkuse as main transcript	n.175+5366G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

38046

AN:

152006

Hom.:

5873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0612

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.411

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.379

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.263

GnomAD3 exomes

AF:

0.306

AC:

74796

AN:

244698

Hom.:

12280

AF XY:

0.301

AC XY:

39953

AN XY:

132782

show subpopulations

Gnomad AFR exome

AF:

0.0566

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.421

Gnomad SAS exome

AF:

0.215

Gnomad FIN exome

AF:

0.378

Gnomad NFE exome

AF:

0.315

Gnomad OTH exome

AF:

0.302

GnomAD4 exome

AF:

0.312

AC:

454517

AN:

1458418

Hom.:

73243

Cov.:

AF XY:

0.308

AC XY:

223760

AN XY:

725560

show subpopulations

Gnomad4 AFR exome

AF:

0.0506

Gnomad4 AMR exome

AF:

0.361

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.405

Gnomad4 SAS exome

AF:

0.216

Gnomad4 FIN exome

AF:

0.370

Gnomad4 NFE exome

AF:

0.320

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.250

AC:

38028

AN:

152124

Hom.:

5867

Cov.:

AF XY:

0.253

AC XY:

18809

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0610

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.311

Gnomad4 EAS

AF:

0.412

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.379

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.304

Hom.:

18102

Bravo

AF:

0.242

TwinsUK

AF:

0.320

AC:

1185

ALSPAC

AF:

0.333

AC:

1285

ESP6500AA

AF:

0.0635

AC:

280

ESP6500EA

AF:

0.320

AC:

2756

ExAC

AF:

0.295

AC:

35751

Asia WGS

AF:

0.323

AC:

1124

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.4

DANN

Benign

0.23

DEOGEN2

Benign

0.0019

T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0063

LIST_S2

Benign

0.018

.;T

MetaRNN

Benign

0.0015

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.6

N;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.30

PROVEAN

Benign

2.2

.;N

REVEL

Benign

0.035

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

.;T

Polyphen

0.0

B;B

Vest4

0.013

MPC

0.026

ClinPred

0.00073

GERP RS

2.5

Varity_R

0.022

gMVP

0.073

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.24

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.24

Position offset: 4

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