Variant rs1476860 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001004450.3(OR1B1):c.571C>T(p.Arg191*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,613,450 control chromosomes in the GnomAD database, including 83,449 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 0.26 ( 6514 hom., cov: 31)

Exomes 𝑓: 0.31 ( 76935 hom. )

Consequence

OR1B1
NM_001004450.3 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Variant links:

Genes affected

OR1B1 (HGNC:8181): (olfactory receptor family 1 subfamily B 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

OR1B1 links:

ENSG00000234156 (HGNC:):

ENSG00000234156 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 = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
OR1B1	NM_001004450.3 linkuse as main transcript	c.571C>T	p.Arg191*	stop_gained	2/2	NP_001004450.2	Q8NGR6
OR1B1	NM_001409693.1 linkuse as main transcript	c.571C>T	p.Arg191*	stop_gained	2/2	NP_001396622.1
LOC124902265	XR_007061759.1 linkuse as main transcript	n.345-8141G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
OR1B1	ENST00000623530.2 linkuse as main transcript	c.571C>T	p.Arg191*	stop_gained	2/2	6	ENSP00000485577.2	Q8NGR6
OR1B1	ENST00000707075.1 linkuse as main transcript	c.571C>T	p.Arg191*	stop_gained	2/2		ENSP00000516726.1	A0A9L9PY52
ENSG00000234156	ENST00000419604.1 linkuse as main transcript	n.279-8144G>A		intron_variant		5
ENSG00000234156	ENST00000431442.2 linkuse as main transcript	n.4768-8141G>A		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39796

AN:

151892

Hom.:

6505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0940

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.425

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.594

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.355

AC:

88789

AN:

250020

Hom.:

18459

AF XY:

0.354

AC XY:

47858

AN XY:

135150

show subpopulations

Gnomad AFR exome

AF:

0.0840

Gnomad AMR exome

AF:

0.542

Gnomad ASJ exome

AF:

0.347

Gnomad EAS exome

AF:

0.611

Gnomad SAS exome

AF:

0.461

Gnomad FIN exome

AF:

0.275

Gnomad NFE exome

AF:

0.284

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.312

AC:

456352

AN:

1461440

Hom.:

76935

Cov.:

AF XY:

0.316

AC XY:

229406

AN XY:

726994

show subpopulations

Gnomad4 AFR exome

AF:

0.0805

Gnomad4 AMR exome

AF:

0.529

Gnomad4 ASJ exome

AF:

0.350

Gnomad4 EAS exome

AF:

0.599

Gnomad4 SAS exome

AF:

0.458

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.290

Gnomad4 OTH exome

AF:

0.309

GnomAD4 genome

AF:

0.262

AC:

39820

AN:

152010

Hom.:

6514

Cov.:

AF XY:

0.270

AC XY:

20086

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.0940

Gnomad4 AMR

AF:

0.426

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.593

Gnomad4 SAS

AF:

0.460

Gnomad4 FIN

AF:

0.267

Gnomad4 NFE

AF:

0.284

Gnomad4 OTH

AF:

0.286

Alfa

AF:

0.293

Hom.:

17850

Bravo

AF:

0.264

TwinsUK

AF:

0.294

AC:

1090

ALSPAC

AF:

0.301

AC:

1160

ESP6500AA

AF:

0.0903

AC:

398

ESP6500EA

AF:

0.297

AC:

2554

ExAC

AF:

0.340

AC:

41248

Asia WGS

AF:

0.481

AC:

1672

AN:

3478

EpiCase

AF:

0.288

EpiControl

AF:

0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Uncertain

0.050

CADD

Pathogenic

DANN

Benign

0.93

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.043

GERP RS

-6.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.20

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.20

Position offset: 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