rs3749971

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_030959.3(OR12D3):c.290C>T(p.Thr97Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 1,613,664 control chromosomes in the GnomAD database, including 8,294 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 0.057 ( 383 hom., cov: 32)

Exomes 𝑓: 0.095 ( 7911 hom. )

Consequence

OR12D3
NM_030959.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Publications

64 publications found

Variant links:

Genes affected

OR12D3 (HGNC:13963): (olfactory receptor family 12 subfamily D member 3) 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]

OR12D3 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=0.003885895).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR12D3	NM_030959.3 link	c.290C>T	p.Thr97Ile	missense_variant	Exon 1 of 1	ENST00000396806.3	NP_112221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR12D3	ENST00000396806.3 link	c.290C>T	p.Thr97Ile	missense_variant	Exon 1 of 1	6	NM_030959.3	ENSP00000380023.3
OR5V1	ENST00000377154.1 link	c.-82-18721C>T		intron_variant	Intron 3 of 3	6		ENSP00000366359.1

Frequencies

GnomAD3 genomes

AF:

0.0570

AC:

8669

AN:

152086

Hom.:

383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0177

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.0263

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.0285

Gnomad SAS

AF:

0.0162

Gnomad FIN

AF:

0.0445

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0945

Gnomad OTH

AF:

0.0411

GnomAD2 exomes

AF:

0.0548

AC:

13520

AN:

246924

AF XY:

0.0556

show subpopulations

Gnomad AFR exome

AF:

0.0198

Gnomad AMR exome

AF:

0.0188

Gnomad ASJ exome

AF:

0.0377

Gnomad EAS exome

AF:

0.0133

Gnomad FIN exome

AF:

0.0446

Gnomad NFE exome

AF:

0.0916

Gnomad OTH exome

AF:

0.0536

GnomAD4 exome

AF:

0.0953

AC:

139284

AN:

1461460

Hom.:

7911

Cov.:

AF XY:

0.0925

AC XY:

67280

AN XY:

727056

show subpopulations

African (AFR)

AF:

0.0182

AC:

609

AN:

33480

American (AMR)

AF:

0.0192

AC:

858

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0389

AC:

1017

AN:

26134

East Asian (EAS)

AF:

0.0506

AC:

2010

AN:

39700

South Asian (SAS)

AF:

0.0178

AC:

1534

AN:

86256

European-Finnish (FIN)

AF:

0.0463

AC:

2457

AN:

53074

Middle Eastern (MID)

AF:

0.0324

AC:

187

AN:

5768

European-Non Finnish (NFE)

AF:

0.113

AC:

125867

AN:

1111930

Other (OTH)

AF:

0.0786

AC:

4745

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

7441

14883

22324

29766

37207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4692

9384

14076

18768

23460

<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:

0.0569

AC:

8667

AN:

152204

Hom.:

383

Cov.:

AF XY:

0.0517

AC XY:

3844

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0177

AC:

736

AN:

41524

American (AMR)

AF:

0.0262

AC:

400

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0415

AC:

144

AN:

3472

East Asian (EAS)

AF:

0.0286

AC:

148

AN:

5172

South Asian (SAS)

AF:

0.0160

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0445

AC:

472

AN:

10604

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0945

AC:

6425

AN:

68002

Other (OTH)

AF:

0.0407

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

406

812

1217

1623

2029

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0839

Hom.:

3008

Bravo

AF:

0.0538

TwinsUK

AF:

0.133

AC:

493

ALSPAC

AF:

0.119

AC:

459

ESP6500AA

AF:

0.0235

AC:

ESP6500EA

AF:

0.0951

AC:

515

ExAC

AF:

0.0538

AC:

6452

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.0901

EpiControl

AF:

0.0853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.7

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.0065

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.72

FATHMM_MKL

Benign

0.021

MetaRNN

Benign

0.0039

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.1

PhyloP100

1.2

PrimateAI

Benign

0.25

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.052

Sift

Benign

0.12

Sift4G

Benign

0.11

Polyphen

0.022

Vest4

0.051

MPC

0.19

ClinPred

0.00055

GERP RS

2.3

PromoterAI

0.0055

Neutral

(source)

Varity_R

0.063

gMVP

0.046

Mutation Taster

=97/3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over