Variant 11-124023281-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001001953.1(OR10G9):c.269C>T(p.Ala90Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 1,529,246 control chromosomes in the GnomAD database, including 55,335 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3368 hom., cov: 24)

Exomes 𝑓: 0.29 ( 51967 hom. )

Consequence

OR10G9
NM_001001953.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.93

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008943349).

BP6

Variant 11-124023281-C-T is Benign according to our data. Variant chr11-124023281-C-T is described in ClinVar as [Benign]. Clinvar id is 769812.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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.269C>T	p.Ala90Val	missense_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.269C>T	p.Ala90Val	missense_variant	1/1	6	NM_001001953.1	ENSP00000364164.1		Q8NGN4

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

32760

AN:

147190

Hom.:

3368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0729

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.275

AC:

61267

AN:

222970

Hom.:

6247

AF XY:

0.272

AC XY:

32893

AN XY:

120790

show subpopulations

Gnomad AFR exome

AF:

0.0628

Gnomad AMR exome

AF:

0.353

Gnomad ASJ exome

AF:

0.263

Gnomad EAS exome

AF:

0.338

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.307

Gnomad NFE exome

AF:

0.278

Gnomad OTH exome

AF:

0.274

GnomAD4 exome

AF:

0.290

AC:

400738

AN:

1381940

Hom.:

51967

Cov.:

AF XY:

0.288

AC XY:

197715

AN XY:

686438

show subpopulations

Gnomad4 AFR exome

AF:

0.0590

Gnomad4 AMR exome

AF:

0.352

Gnomad4 ASJ exome

AF:

0.267

Gnomad4 EAS exome

AF:

0.328

Gnomad4 SAS exome

AF:

0.237

Gnomad4 FIN exome

AF:

0.328

Gnomad4 NFE exome

AF:

0.297

Gnomad4 OTH exome

AF:

0.282

GnomAD4 genome

AF:

0.223

AC:

32778

AN:

147306

Hom.:

3368

Cov.:

AF XY:

0.226

AC XY:

16224

AN XY:

71694

show subpopulations

Gnomad4 AFR

AF:

0.0729

Gnomad4 AMR

AF:

0.274

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.311

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.214

Alfa

AF:

0.259

Hom.:

816

ExAC

AF:

0.255

AC:

30488

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	Jun 22, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.73

CADD

Benign

4.9

DANN

Benign

0.51

DEOGEN2

Benign

0.00042

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.044

MetaRNN

Benign

0.0089

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.46

PrimateAI

Benign

0.22

PROVEAN

Benign

-0.29

REVEL

Benign

0.038

Sift

Benign

0.42

Sift4G

Benign

0.58

Polyphen

0.011

Vest4

0.016

MPC

0.30

ClinPred

0.0021

GERP RS

0.22

Varity_R

0.036

gMVP

0.043

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