Genetic Variant OR10G9:p.Met134Val (chr11-124023412-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_001001953.1(OR10G9):c.400A>G(p.Met134Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 1,592,192 control chromosomes in the GnomAD database, including 112,856 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 (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.29 ( 7636 hom., cov: 24)

Exomes 𝑓: 0.37 ( 105220 hom. )

Consequence

OR10G9
NM_001001953.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.39

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=8.300841E-4).

BP6

Variant 11-124023412-A-G is Benign according to our data. Variant chr11-124023412-A-G is described in ClinVar as [Benign]. Clinvar id is 769378.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10G9	NM_001001953.1 link	c.400A>G	p.Met134Val	missense_variant	Exon 1 of 1	ENST00000375024.1	NP_001001953.1	Q8NGN4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR10G9	ENST00000375024.1 link	c.400A>G	p.Met134Val	missense_variant	Exon 1 of 1	6	NM_001001953.1	ENSP00000364164.1		Q8NGN4

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44036

AN:

149846

Hom.:

7642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.401

Gnomad OTH

AF:

0.334

GnomAD3 exomes

AF:

0.318

AC:

79046

AN:

248192

Hom.:

14072

AF XY:

0.327

AC XY:

43865

AN XY:

134236

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.350

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.271

Gnomad FIN exome

AF:

0.334

Gnomad NFE exome

AF:

0.406

Gnomad OTH exome

AF:

0.352

GnomAD4 exome

AF:

0.372

AC:

536513

AN:

1442230

Hom.:

105220

Cov.:

AF XY:

0.371

AC XY:

266393

AN XY:

717806

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.252

Gnomad4 ASJ exome

AF:

0.354

Gnomad4 EAS exome

AF:

0.171

Gnomad4 SAS exome

AF:

0.269

Gnomad4 FIN exome

AF:

0.336

Gnomad4 NFE exome

AF:

0.403

Gnomad4 OTH exome

AF:

0.353

GnomAD4 genome

AF:

0.294

AC:

44019

AN:

149962

Hom.:

7636

Cov.:

AF XY:

0.286

AC XY:

20908

AN XY:

73072

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.368

Gnomad4 EAS

AF:

0.150

Gnomad4 SAS

AF:

0.253

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.401

Gnomad4 OTH

AF:

0.328

Alfa

AF:

0.350

Hom.:

1634

Bravo

AF:

0.287

ESP6500AA

AF:

0.119

AC:

525

ESP6500EA

AF:

0.382

AC:

3277

ExAC

AF:

0.324

AC:

39300

Asia WGS

AF:

0.186

AC:

650

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 14, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.058

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.010

DANN

Benign

0.32

DEOGEN2

Benign

0.00033

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.080

LIST_S2

Benign

0.075

MetaRNN

Benign

0.00083

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-1.4

PrimateAI

Benign

0.26

PROVEAN

Benign

1.2

REVEL

Benign

0.021

Sift

Benign

0.17

Sift4G

Benign

0.41

Polyphen

0.0

Vest4

0.017

MPC

0.29

ClinPred

0.016

GERP RS

-7.0

Varity_R

0.065

gMVP

0.18

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