dbSNP rs1476860: OR1B1:p.Arg191* (chr9-122628962-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000623530.2(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
ENST00000623530.2 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Publications

36 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	Protein	UniProt
OR1B1	NM_001004450.3 link	c.571C>T	p.Arg191*	stop_gained	Exon 2 of 2	NP_001004450.2	Q8NGR6
OR1B1	NM_001409693.1 link	c.571C>T	p.Arg191*	stop_gained	Exon 2 of 2	NP_001396622.1
LOC124902265	XR_007061759.1 link	n.345-8141G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR1B1	ENST00000623530.2 link	c.571C>T	p.Arg191*	stop_gained	Exon 2 of 2	6		ENSP00000485577.2		Q8NGR6

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

GnomAD2 exomes

AF:

0.355

AC:

88789

AN:

250020

AF XY:

0.354

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 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

African (AFR)

AF:

0.0805

AC:

2693

AN:

33472

American (AMR)

AF:

0.529

AC:

23626

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

9140

AN:

26130

East Asian (EAS)

AF:

0.599

AC:

23766

AN:

39680

South Asian (SAS)

AF:

0.458

AC:

39532

AN:

86238

European-Finnish (FIN)

AF:

0.281

AC:

15004

AN:

53400

Middle Eastern (MID)

AF:

0.281

AC:

1623

AN:

5768

European-Non Finnish (NFE)

AF:

0.290

AC:

322301

AN:

1111702

Other (OTH)

AF:

0.309

AC:

18667

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

17954

35908

53861

71815

89769

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10974

21948

32922

43896

54870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.262

AC:

39820

AN:

152010

Hom.:

6514

Cov.:

AF XY:

0.270

AC XY:

20086

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.0940

AC:

3899

AN:

41488

American (AMR)

AF:

0.426

AC:

6499

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

1199

AN:

3468

East Asian (EAS)

AF:

0.593

AC:

3049

AN:

5142

South Asian (SAS)

AF:

0.460

AC:

2218

AN:

4818

European-Finnish (FIN)

AF:

0.267

AC:

2822

AN:

10560

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19321

AN:

67968

Other (OTH)

AF:

0.286

AC:

601

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1384

2768

4153

5537

6921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.289

Hom.:

34419

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

(source)

DANN

Benign

0.93

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.043

PhyloP100

-0.17

GERP RS

-6.0

Mutation Taster

=198/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over