Variant rs12364099 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001005188.1(OR6X1):c.569C>A(p.Thr190Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,614,032 control chromosomes in the GnomAD database, including 17,430 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.11 ( 1253 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16177 hom. )

Consequence

OR6X1
NM_001005188.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.73

Variant links:

Genes affected

OR6X1 (HGNC:14737): (olfactory receptor family 6 subfamily X 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]

OR6X1 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=0.0013703108).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6X1	NM_001005188.1 linkuse as main transcript	c.569C>A	p.Thr190Asn	missense_variant	1/1	ENST00000327930.3	NP_001005188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6X1	ENST00000327930.3 linkuse as main transcript	c.569C>A	p.Thr190Asn	missense_variant	1/1		NM_001005188.1	ENSP00000333724	P1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17038

AN:

152092

Hom.:

1256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0371

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.0200

Gnomad SAS

AF:

0.0965

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.136

GnomAD3 exomes

AF:

0.123

AC:

30855

AN:

251380

Hom.:

2267

AF XY:

0.127

AC XY:

17285

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.0325

Gnomad AMR exome

AF:

0.0749

Gnomad ASJ exome

AF:

0.231

Gnomad EAS exome

AF:

0.0245

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.156

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.143

AC:

209595

AN:

1461822

Hom.:

16177

Cov.:

AF XY:

0.144

AC XY:

104404

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.0353

Gnomad4 AMR exome

AF:

0.0800

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.0198

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.143

Gnomad4 NFE exome

AF:

0.154

Gnomad4 OTH exome

AF:

0.143

GnomAD4 genome

AF:

0.112

AC:

17032

AN:

152210

Hom.:

1253

Cov.:

AF XY:

0.110

AC XY:

8215

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.0371

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.0199

Gnomad4 SAS

AF:

0.0966

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.150

Hom.:

4530

Bravo

AF:

0.105

TwinsUK

AF:

0.151

AC:

559

ALSPAC

AF:

0.168

AC:

646

ESP6500AA

AF:

0.0425

AC:

187

ESP6500EA

AF:

0.156

AC:

1342

ExAC

AF:

0.122

AC:

14797

Asia WGS

AF:

0.0560

AC:

194

AN:

3478

EpiCase

AF:

0.163

EpiControl

AF:

0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0091

Eigen

Benign

-0.55

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.31

LIST_S2

Benign

0.66

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.0

MutationAssessor

Pathogenic

3.1

MutationTaster

Benign

0.89

PrimateAI

Benign

0.23

PROVEAN

Uncertain

-4.3

REVEL

Benign

0.10

Sift

Uncertain

0.0010

Sift4G

Uncertain

0.011

Polyphen

0.029

Vest4

0.081

MPC

0.15

ClinPred

0.073

GERP RS

3.5

Varity_R

0.63

gMVP

0.25

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