Variant 11-124023429-A-G 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_001001953.1(OR10G9):c.417A>G(p.Arg139Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 1,576,828 control chromosomes in the GnomAD database, including 593,933 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.87 ( 57065 hom., cov: 24)

Exomes 𝑓: 0.86 ( 536868 hom. )

Consequence

OR10G9
NM_001001953.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.81

Variant links:

Genes affected

OR10G9 (HGNC:15129): (olfactory receptor family 10 subfamily G member 9) 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]

OR10G9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 11-124023429-A-G is Benign according to our data. Variant chr11-124023429-A-G is described in ClinVar as [Benign]. Clinvar id is 768493.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.81 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR10G9	NM_001001953.1 linkuse as main transcript	c.417A>G	p.Arg139Arg	synonymous_variant	1/1	ENST00000375024.1	NP_001001953.1	Q8NGN4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR10G9	ENST00000375024.1 linkuse as main transcript	c.417A>G	p.Arg139Arg	synonymous_variant	1/1	6	NM_001001953.1	ENSP00000364164.1		Q8NGN4

Frequencies

GnomAD3 genomes

AF:

0.872

AC:

130390

AN:

149514

Hom.:

57016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.909

Gnomad AMI

AF:

0.902

Gnomad AMR

AF:

0.892

Gnomad ASJ

AF:

0.881

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.687

Gnomad FIN

AF:

0.888

Gnomad MID

AF:

0.876

Gnomad NFE

AF:

0.861

Gnomad OTH

AF:

0.863

GnomAD3 exomes

AF:

0.864

AC:

206889

AN:

239402

Hom.:

90775

AF XY:

0.855

AC XY:

110634

AN XY:

129446

show subpopulations

Gnomad AFR exome

AF:

0.918

Gnomad AMR exome

AF:

0.923

Gnomad ASJ exome

AF:

0.891

Gnomad EAS exome

AF:

0.815

Gnomad SAS exome

AF:

0.704

Gnomad FIN exome

AF:

0.916

Gnomad NFE exome

AF:

0.877

Gnomad OTH exome

AF:

0.863

GnomAD4 exome

AF:

0.864

AC:

1233576

AN:

1427198

Hom.:

536868

Cov.:

AF XY:

0.859

AC XY:

610262

AN XY:

710698

show subpopulations

Gnomad4 AFR exome

AF:

0.917

Gnomad4 AMR exome

AF:

0.907

Gnomad4 ASJ exome

AF:

0.879

Gnomad4 EAS exome

AF:

0.831

Gnomad4 SAS exome

AF:

0.696

Gnomad4 FIN exome

AF:

0.898

Gnomad4 NFE exome

AF:

0.874

Gnomad4 OTH exome

AF:

0.863

GnomAD4 genome

AF:

0.872

AC:

130494

AN:

149630

Hom.:

57065

Cov.:

AF XY:

0.871

AC XY:

63568

AN XY:

72952

show subpopulations

Gnomad4 AFR

AF:

0.909

Gnomad4 AMR

AF:

0.892

Gnomad4 ASJ

AF:

0.881

Gnomad4 EAS

AF:

0.791

Gnomad4 SAS

AF:

0.688

Gnomad4 FIN

AF:

0.888

Gnomad4 NFE

AF:

0.861

Gnomad4 OTH

AF:

0.856

Alfa

AF:

0.865

Hom.:

10326

Bravo

AF:

0.879

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 14, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.35

DANN

Benign

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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