dbSNP rs1151687: OR2G2:p.Val120Leu (chr1-247588717-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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

Publications

27 publications found

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:

ENSG00000236817 (HGNC:):

ENSG00000236817 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001915.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR2G2	NM_001001915.1	MANE Select	c.358G>C	p.Val120Leu	missense	Exon 1 of 1	NP_001001915.1	Q8NGZ5
LOC102724446	NR_188589.1		n.226-22766C>G		intron	N/A
LOC102724446	NR_188590.1		n.438-22766C>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR2G2	ENST00000320065.1	TSL:6 MANE Select	c.358G>C	p.Val120Leu	missense	Exon 1 of 1	ENSP00000326349.1	Q8NGZ5
ENSG00000236817	ENST00000435333.6	TSL:3	n.295-22766C>G		intron	N/A
ENSG00000236817	ENST00000446347.1	TSL:2	n.438-22766C>G		intron	N/A

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

GnomAD2 exomes

AF:

0.689

AC:

172741

AN:

250850

AF XY:

0.699

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 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

African (AFR)

AF:

0.227

AC:

7590

AN:

33480

American (AMR)

AF:

0.716

AC:

32040

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.747

AC:

19531

AN:

26132

East Asian (EAS)

AF:

0.775

AC:

30779

AN:

39700

South Asian (SAS)

AF:

0.753

AC:

64973

AN:

86256

European-Finnish (FIN)

AF:

0.678

AC:

36237

AN:

53416

Middle Eastern (MID)

AF:

0.635

AC:

3660

AN:

5766

European-Non Finnish (NFE)

AF:

0.707

AC:

786386

AN:

1111998

Other (OTH)

AF:

0.681

AC:

41148

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

20212

40424

60636

80848

101060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19680

39360

59040

78720

98400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.580

AC:

88099

AN:

151978

Hom.:

29010

Cov.:

AF XY:

0.585

AC XY:

43424

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.244

AC:

10114

AN:

41476

American (AMR)

AF:

0.676

AC:

10315

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.745

AC:

2582

AN:

3466

East Asian (EAS)

AF:

0.780

AC:

4021

AN:

5154

South Asian (SAS)

AF:

0.760

AC:

3660

AN:

4818

European-Finnish (FIN)

AF:

0.672

AC:

7089

AN:

10544

Middle Eastern (MID)

AF:

0.613

AC:

179

AN:

292

European-Non Finnish (NFE)

AF:

0.708

AC:

48117

AN:

67946

Other (OTH)

AF:

0.616

AC:

1299

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1565

3130

4696

6261

7826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

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

PhyloP100

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

PromoterAI

-0.0076

Neutral

(source)

Varity_R

0.36

gMVP

0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over