dbSNP rs75010552: OR2T11:p.Met203Arg (chr1-248626521-A-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001001964.2(OR2T11):c.608T>G(p.Met203Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00775 in 1,569,092 control chromosomes in the GnomAD database, including 1,446 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0053 ( 85 hom., cov: 28)

Exomes 𝑓: 0.0080 ( 1361 hom. )

Consequence

OR2T11
NM_001001964.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44

Publications

11 publications found

Variant links:

Genes affected

OR2T11 (HGNC:19574): (olfactory receptor family 2 subfamily T member 11) 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]

OR2T11 links:

ENSG00000229255 (HGNC:):

ENSG00000229255 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 85 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2T11	NM_001001964.2 link	c.608T>G	p.Met203Arg	missense_variant	Exon 2 of 2	ENST00000641193.1	NP_001001964.1	Q8NH01

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2T11	ENST00000641193.1 link	c.608T>G	p.Met203Arg	missense_variant	Exon 2 of 2		NM_001001964.2	ENSP00000492951.1		Q8NH01

Frequencies

GnomAD3 genomes

AF:

0.00529

AC:

757

AN:

143198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00152

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00143

Gnomad ASJ

AF:

0.00764

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0110

Gnomad FIN

AF:

0.00212

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00861

Gnomad OTH

AF:

0.00646

GnomAD2 exomes

AF:

0.00648

AC:

1582

AN:

244134

AF XY:

0.00698

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00118

Gnomad ASJ exome

AF:

0.0125

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00286

Gnomad NFE exome

AF:

0.00812

Gnomad OTH exome

AF:

0.00533

GnomAD4 exome

AF:

0.00800

AC:

11404

AN:

1425772

Hom.:

1361

Cov.:

AF XY:

0.00823

AC XY:

5840

AN XY:

709824

show subpopulations

African (AFR)

AF:

0.00111

AC:

AN:

30596

American (AMR)

AF:

0.00142

AC:

AN:

43688

Ashkenazi Jewish (ASJ)

AF:

0.0112

AC:

289

AN:

25730

East Asian (EAS)

AF:

0.00

AC:

AN:

38694

South Asian (SAS)

AF:

0.0130

AC:

1096

AN:

84300

European-Finnish (FIN)

AF:

0.00310

AC:

159

AN:

51322

Middle Eastern (MID)

AF:

0.00616

AC:

AN:

5678

European-Non Finnish (NFE)

AF:

0.00858

AC:

9321

AN:

1086676

Other (OTH)

AF:

0.00690

AC:

408

AN:

59088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

516

1032

1549

2065

2581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.00528

AC:

757

AN:

143320

Hom.:

Cov.:

AF XY:

0.00512

AC XY:

358

AN XY:

69990

show subpopulations

African (AFR)

AF:

0.00151

AC:

AN:

36398

American (AMR)

AF:

0.00143

AC:

AN:

14716

Ashkenazi Jewish (ASJ)

AF:

0.00764

AC:

AN:

3402

East Asian (EAS)

AF:

0.00

AC:

AN:

4940

South Asian (SAS)

AF:

0.0110

AC:

AN:

4542

European-Finnish (FIN)

AF:

0.00212

AC:

AN:

9904

Middle Eastern (MID)

AF:

0.00342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00861

AC:

570

AN:

66206

Other (OTH)

AF:

0.00639

AC:

AN:

2034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

126

158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00834

Hom.:

100

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.00649

AC:

ESP6500AA

AF:

0.00244

AC:

ESP6500EA

AF:

0.00850

AC:

ExAC

AF:

0.00679

AC:

808

Asia WGS

AF:

0.00387

AC:

AN:

3374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.38

CADD

Uncertain

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.014

T;T

Eigen

Benign

0.075

Eigen_PC

Benign

-0.088

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.71

.;T

MetaRNN

Benign

0.0074

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.7

L;L

PhyloP100

1.4

PrimateAI

Benign

0.22

Polyphen

1.0

D;D

ClinPred

0.092

GERP RS

3.3

Varity_R

0.70

gMVP

0.64

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.25

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.25

Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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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