Variant 9-122629491-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001004450.3(OR1B1):c.41_42insT(p.Leu14PhefsTer9) variant causes a frameshift change. The variant allele was found at a frequency of 0.49 in 1,608,368 control chromosomes in the GnomAD database, including 196,273 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.46 ( 16793 hom., cov: 0)

Exomes 𝑓: 0.49 ( 179480 hom. )

Consequence

OR1B1
NM_001004450.3 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.75

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-122629491-C-CA is Benign according to our data. Variant chr9-122629491-C-CA is described in ClinVar as [Benign]. Clinvar id is 403271.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
OR1B1	NM_001004450.3 linkuse as main transcript	c.41_42insT	p.Leu14PhefsTer9	frameshift_variant	2/2	ENST00000623530.2
LOC124902265	XR_007061759.1 linkuse as main transcript	n.345-7605dup		intron_variant, non_coding_transcript_variant
OR1B1	NM_001409693.1 linkuse as main transcript	c.41_42insT	p.Leu14PhefsTer9	frameshift_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
OR1B1	ENST00000623530.2 linkuse as main transcript	c.41_42insT	p.Leu14PhefsTer9	frameshift_variant	2/2		NM_001004450.3	P1
	ENST00000431442.2 linkuse as main transcript	n.4768-7605dup		intron_variant, non_coding_transcript_variant		3
OR1B1	ENST00000707075.1 linkuse as main transcript	c.41_42insT	p.Leu14PhefsTer9	frameshift_variant	2/2			P1
	ENST00000419604.1 linkuse as main transcript	n.279-7608dup		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70306

AN:

151482

Hom.:

16788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.414

Gnomad AMI

AF:

0.689

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.616

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.434

GnomAD3 exomes

AF:

0.452

AC:

111099

AN:

245860

Hom.:

26307

AF XY:

0.460

AC XY:

61192

AN XY:

132972

show subpopulations

Gnomad AFR exome

AF:

0.422

Gnomad AMR exome

AF:

0.271

Gnomad ASJ exome

AF:

0.431

Gnomad EAS exome

AF:

0.322

Gnomad SAS exome

AF:

0.448

Gnomad FIN exome

AF:

0.595

Gnomad NFE exome

AF:

0.508

Gnomad OTH exome

AF:

0.451

GnomAD4 exome

AF:

0.492

AC:

717437

AN:

1456768

Hom.:

179480

Cov.:

AF XY:

0.492

AC XY:

356417

AN XY:

724636

show subpopulations

Gnomad4 AFR exome

AF:

0.416

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.426

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.447

Gnomad4 FIN exome

AF:

0.584

Gnomad4 NFE exome

AF:

0.510

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

AF:

0.464

AC:

70337

AN:

151600

Hom.:

16793

Cov.:

AF XY:

0.468

AC XY:

34625

AN XY:

74060

show subpopulations

Gnomad4 AFR

AF:

0.414

Gnomad4 AMR

AF:

0.339

Gnomad4 ASJ

AF:

0.428

Gnomad4 EAS

AF:

0.339

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.616

Gnomad4 NFE

AF:

0.509

Gnomad4 OTH

AF:

0.435

Alfa

AF:

0.381

Hom.:

1697

Asia WGS

AF:

0.381

AC:

1329

AN:

3478

EpiCase

AF:

0.492

EpiControl

AF:

0.493

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 896/2178=41.1% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over