rs4478844

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_001004491.2(OR2AK2):c.562G>A(p.Val188Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 1,608,454 control chromosomes in the GnomAD database, including 304,847 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 21840 hom., cov: 32)

Exomes 𝑓: 0.62 ( 283007 hom. )

Consequence

OR2AK2
NM_001004491.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.930

Publications

44 publications found

Variant links:

Genes affected

OR2AK2 (HGNC:19569): (olfactory receptor family 2 subfamily AK 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]

OR2AK2 links:

OR2L13 (HGNC:19578): (olfactory receptor family 2 subfamily L member 13) 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]

OR2L13 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.161648E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004491.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
OR2AK2	NM_001004491.2	MANE Select	c.562G>A	p.Val188Met	missense	Exon 1 of 1	NP_001004491.2
OR2L13	NM_001304535.3		c.-19+28554G>A		intron	N/A	NP_001291464.1
OR2L13	NM_175911.5		c.-144+28554G>A		intron	N/A	NP_787107.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2AK2	ENST00000366480.5	TSL:6 MANE Select	c.562G>A	p.Val188Met	missense	Exon 1 of 1	ENSP00000355436.4

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

75683

AN:

151808

Hom.:

21844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.561

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.648

Gnomad MID

AF:

0.640

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.544

GnomAD2 exomes

AF:

0.573

AC:

141548

AN:

247002

AF XY:

0.579

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.594

Gnomad ASJ exome

AF:

0.627

Gnomad EAS exome

AF:

0.458

Gnomad FIN exome

AF:

0.650

Gnomad NFE exome

AF:

0.636

Gnomad OTH exome

AF:

0.612

GnomAD4 exome

AF:

0.617

AC:

898631

AN:

1456528

Hom.:

283007

Cov.:

AF XY:

0.615

AC XY:

445470

AN XY:

724120

show subpopulations

African (AFR)

AF:

0.168

AC:

5623

AN:

33410

American (AMR)

AF:

0.590

AC:

26190

AN:

44416

Ashkenazi Jewish (ASJ)

AF:

0.618

AC:

15905

AN:

25756

East Asian (EAS)

AF:

0.408

AC:

16190

AN:

39640

South Asian (SAS)

AF:

0.524

AC:

44750

AN:

85366

European-Finnish (FIN)

AF:

0.650

AC:

34567

AN:

53188

Middle Eastern (MID)

AF:

0.583

AC:

3348

AN:

5738

European-Non Finnish (NFE)

AF:

0.646

AC:

715928

AN:

1108866

Other (OTH)

AF:

0.601

AC:

36130

AN:

60148

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

17214

34427

51641

68854

86068

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18712

37424

56136

74848

93560

<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:

0.498

AC:

75674

AN:

151926

Hom.:

21840

Cov.:

AF XY:

0.498

AC XY:

36970

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.187

AC:

7761

AN:

41402

American (AMR)

AF:

0.582

AC:

8873

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2191

AN:

3472

East Asian (EAS)

AF:

0.449

AC:

2317

AN:

5158

South Asian (SAS)

AF:

0.525

AC:

2527

AN:

4816

European-Finnish (FIN)

AF:

0.648

AC:

6845

AN:

10556

Middle Eastern (MID)

AF:

0.630

AC:

184

AN:

292

European-Non Finnish (NFE)

AF:

0.637

AC:

43319

AN:

67964

Other (OTH)

AF:

0.543

AC:

1145

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1658

3316

4973

6631

8289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.593

Hom.:

137750

Bravo

AF:

0.480

TwinsUK

AF:

0.648

AC:

2403

ALSPAC

AF:

0.655

AC:

2524

ESP6500AA

AF:

0.194

AC:

856

ESP6500EA

AF:

0.641

AC:

5510

ExAC

AF:

0.563

AC:

68336

Asia WGS

AF:

0.465

AC:

1622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.37

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.76

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0013

Eigen

Benign

-0.24

Eigen_PC

Benign

-0.50

FATHMM_MKL

Benign

0.018

LIST_S2

Benign

0.71

MetaRNN

Benign

0.0000082

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.9

PhyloP100

-0.93

PrimateAI

Benign

0.22

REVEL

Benign

0.045

Polyphen

1.0

MPC

0.24

ClinPred

0.045

GERP RS

0.63

Varity_R

0.29

gMVP

0.10

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