6-29397038-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013936.4(OR12D2):c.339C>G(p.Phe113Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,612,218 control chromosomes in the GnomAD database, including 139,747 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 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 0.36 ( 10567 hom., cov: 32)

Exomes 𝑓: 0.42 ( 129180 hom. )

Consequence

OR12D2
NM_013936.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.488

Publications

32 publications found

Variant links:

Genes affected

OR12D2 (HGNC:8178): (olfactory receptor family 12 subfamily D 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

OR12D2 links:

OR5V1 (HGNC:13972): (olfactory receptor family 5 subfamily V member 1) 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]

OR5V1 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=1.3890862E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR12D2	NM_013936.4 link	c.339C>G	p.Phe113Leu	missense_variant	Exon 2 of 2	ENST00000642051.1	NP_039224.2	P58182A0A126GV87

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
OR12D2	ENST00000642051.1 link	c.339C>G	p.Phe113Leu	missense_variant	Exon 2 of 2		NM_013936.4	ENSP00000493463.1	P58182
OR12D2	ENST00000623183.1 link	c.339C>G	p.Phe113Leu	missense_variant	Exon 1 of 1	6		ENSP00000485112.1	P58182
OR5V1	ENST00000377154.1 link	c.-83+25569G>C		intron_variant	Intron 3 of 3	6		ENSP00000366359.1	Q9UGF6

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54482

AN:

151926

Hom.:

10560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.376

GnomAD2 exomes

AF:

0.391

AC:

96160

AN:

246234

AF XY:

0.388

show subpopulations

Gnomad AFR exome

AF:

0.203

Gnomad AMR exome

AF:

0.392

Gnomad ASJ exome

AF:

0.486

Gnomad EAS exome

AF:

0.325

Gnomad FIN exome

AF:

0.420

Gnomad NFE exome

AF:

0.441

Gnomad OTH exome

AF:

0.407

GnomAD4 exome

AF:

0.416

AC:

607289

AN:

1460174

Hom.:

129180

Cov.:

AF XY:

0.414

AC XY:

300652

AN XY:

726496

show subpopulations

African (AFR)

AF:

0.197

AC:

6598

AN:

33472

American (AMR)

AF:

0.389

AC:

17385

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.485

AC:

12683

AN:

26124

East Asian (EAS)

AF:

0.346

AC:

13729

AN:

39686

South Asian (SAS)

AF:

0.281

AC:

24270

AN:

86250

European-Finnish (FIN)

AF:

0.418

AC:

21901

AN:

52422

Middle Eastern (MID)

AF:

0.360

AC:

2075

AN:

5766

European-Non Finnish (NFE)

AF:

0.436

AC:

484316

AN:

1111386

Other (OTH)

AF:

0.403

AC:

24332

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

20826

41651

62477

83302

104128

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.358

AC:

54494

AN:

152044

Hom.:

10567

Cov.:

AF XY:

0.359

AC XY:

26652

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.204

AC:

8469

AN:

41474

American (AMR)

AF:

0.371

AC:

5674

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.496

AC:

1717

AN:

3464

East Asian (EAS)

AF:

0.345

AC:

1783

AN:

5168

South Asian (SAS)

AF:

0.263

AC:

1268

AN:

4818

European-Finnish (FIN)

AF:

0.428

AC:

4525

AN:

10566

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.437

AC:

29681

AN:

67966

Other (OTH)

AF:

0.372

AC:

786

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1719

3437

5156

6874

8593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.422

Hom.:

4502

Bravo

AF:

0.351

TwinsUK

AF:

0.412

AC:

1527

ALSPAC

AF:

0.439

AC:

1692

ESP6500AA

AF:

0.222

AC:

670

ESP6500EA

AF:

0.445

AC:

2409

ExAC

AF:

0.385

AC:

45495

Asia WGS

AF:

0.255

AC:

889

AN:

3478

EpiCase

AF:

0.432

EpiControl

AF:

0.441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.60

CADD

Benign

1.0

(source)

DANN

Benign

0.28

DEOGEN2

Benign

0.0026

T;T

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0044

LIST_S2

Benign

0.46

.;T

MetaRNN

Benign

0.00014

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-2.9

N;N

PhyloP100

-0.49

PrimateAI

Benign

0.25

Polyphen

0.0

B;B

MutPred

0.13

Gain of disorder (P = 0.1562);Gain of disorder (P = 0.1562);

ClinPred

0.0041

GERP RS

1.0

PromoterAI

-0.030

Neutral

(source)

Varity_R

0.081

gMVP

0.12

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

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6-29397038-C-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over