Variant 2-240045743-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_173351.2(OR6B3):c.330C>T(p.Thr110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 1,375,974 control chromosomes in the GnomAD database, including 3,093 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 840 hom., cov: 26)

Exomes 𝑓: 0.045 ( 2253 hom. )

Consequence

OR6B3
NM_173351.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -5.92

Variant links:

Genes affected

OR6B3 (HGNC:15042): (olfactory receptor family 6 subfamily B member 3) 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]

OR6B3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 2-240045743-G-A is Benign according to our data. Variant chr2-240045743-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 767875.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-5.92 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6B3	NM_173351.2 linkuse as main transcript	c.330C>T	p.Thr110=	synonymous_variant	3/3	ENST00000641019.2	NP_775486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6B3	ENST00000641019.2 linkuse as main transcript	c.330C>T	p.Thr110=	synonymous_variant	3/3		NM_173351.2	ENSP00000493035	P1

Frequencies

GnomAD3 genomes

AF:

0.0823

AC:

12295

AN:

149450

Hom.:

833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.0486

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.0815

Gnomad EAS

AF:

0.00293

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.00533

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0352

Gnomad OTH

AF:

0.0835

GnomAD3 exomes

AF:

0.0686

AC:

15530

AN:

226266

Hom.:

955

AF XY:

0.0666

AC XY:

8232

AN XY:

123528

show subpopulations

Gnomad AFR exome

AF:

0.175

Gnomad AMR exome

AF:

0.157

Gnomad ASJ exome

AF:

0.0821

Gnomad EAS exome

AF:

0.00233

Gnomad SAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.00859

Gnomad NFE exome

AF:

0.0353

Gnomad OTH exome

AF:

0.0623

GnomAD4 exome

AF:

0.0451

AC:

55285

AN:

1226408

Hom.:

2253

Cov.:

AF XY:

0.0467

AC XY:

29021

AN XY:

620854

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.158

Gnomad4 ASJ exome

AF:

0.0845

Gnomad4 EAS exome

AF:

0.00133

Gnomad4 SAS exome

AF:

0.111

Gnomad4 FIN exome

AF:

0.00931

Gnomad4 NFE exome

AF:

0.0320

Gnomad4 OTH exome

AF:

0.0530

GnomAD4 genome

AF:

0.0825

AC:

12333

AN:

149566

Hom.:

840

Cov.:

AF XY:

0.0828

AC XY:

6038

AN XY:

72882

show subpopulations

Gnomad4 AFR

AF:

0.173

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.0815

Gnomad4 EAS

AF:

0.00313

Gnomad4 SAS

AF:

0.112

Gnomad4 FIN

AF:

0.00533

Gnomad4 NFE

AF:

0.0352

Gnomad4 OTH

AF:

0.0831

Alfa

AF:

0.0632

Hom.:

Bravo

AF:

0.0962

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 22, 2017	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.70

DANN

Benign

0.91

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