Variant rs1151687 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001001915.1(OR2G2):c.358G>C(p.Val120Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 1,613,842 control chromosomes in the GnomAD database, including 391,182 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.58 ( 29010 hom., cov: 31)

Exomes 𝑓: 0.70 ( 362172 hom. )

Consequence

OR2G2
NM_001001915.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.999

Variant links:

Genes affected

OR2G2 (HGNC:15007): (olfactory receptor family 2 subfamily G member 2) 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]

OR2G2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.532855E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2G2	NM_001001915.1 linkuse as main transcript	c.358G>C	p.Val120Leu	missense_variant	1/1	ENST00000320065.1
LOC102724446	XR_426948.4 linkuse as main transcript	n.226-22766C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
OR2G2	ENST00000320065.1 linkuse as main transcript	c.358G>C	p.Val120Leu	missense_variant	1/1		NM_001001915.1	P1
	ENST00000435333.5 linkuse as main transcript	n.226-22766C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000446347.1 linkuse as main transcript	n.438-22766C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

88055

AN:

151860

Hom.:

28995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.793

Gnomad AMR

AF:

0.676

Gnomad ASJ

AF:

0.745

Gnomad EAS

AF:

0.781

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.672

Gnomad MID

AF:

0.602

Gnomad NFE

AF:

0.708

Gnomad OTH

AF:

0.615

GnomAD3 exomes

AF:

0.689

AC:

172741

AN:

250850

Hom.:

61482

AF XY:

0.699

AC XY:

94733

AN XY:

135544

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.721

Gnomad ASJ exome

AF:

0.755

Gnomad EAS exome

AF:

0.798

Gnomad SAS exome

AF:

0.756

Gnomad FIN exome

AF:

0.675

Gnomad NFE exome

AF:

0.704

Gnomad OTH exome

AF:

0.705

GnomAD4 exome

AF:

0.699

AC:

1022344

AN:

1461864

Hom.:

362172

Cov.:

AF XY:

0.703

AC XY:

510939

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.227

Gnomad4 AMR exome

AF:

0.716

Gnomad4 ASJ exome

AF:

0.747

Gnomad4 EAS exome

AF:

0.775

Gnomad4 SAS exome

AF:

0.753

Gnomad4 FIN exome

AF:

0.678

Gnomad4 NFE exome

AF:

0.707

Gnomad4 OTH exome

AF:

0.681

GnomAD4 genome

AF:

0.580

AC:

88099

AN:

151978

Hom.:

29010

Cov.:

AF XY:

0.585

AC XY:

43424

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.244

Gnomad4 AMR

AF:

0.676

Gnomad4 ASJ

AF:

0.745

Gnomad4 EAS

AF:

0.780

Gnomad4 SAS

AF:

0.760

Gnomad4 FIN

AF:

0.672

Gnomad4 NFE

AF:

0.708

Gnomad4 OTH

AF:

0.616

Alfa

AF:

0.693

Hom.:

28000

Bravo

AF:

0.566

TwinsUK

AF:

0.701

AC:

2599

ALSPAC

AF:

0.709

AC:

2732

ESP6500AA

AF:

0.251

AC:

1107

ESP6500EA

AF:

0.708

AC:

6090

ExAC

AF:

0.678

AC:

82289

Asia WGS

AF:

0.720

AC:

2505

AN:

3478

EpiCase

AF:

0.703

EpiControl

AF:

0.710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

Cadd

Benign

Dann

Uncertain

0.99

DEOGEN2

Benign

0.0082

Eigen

Benign

-0.40

Eigen_PC

Benign

-0.41

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.58

MetaRNN

Benign

8.5e-7

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.053

Sift

Uncertain

0.0040

Sift4G

Uncertain

0.055

Polyphen

0.11

Vest4

0.084

MutPred

0.11

Loss of catalytic residue at V120 (P = 0.0719);

MPC

0.080

ClinPred

0.027

GERP RS

3.4

Varity_R

0.36

gMVP

0.13

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over