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

Variant summary

Our verdict is Likely benign. Variant got -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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -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

GnomAD3 exomes

AF:

0.00648

AC:

1582

AN:

244134

Hom.:

190

AF XY:

0.00698

AC XY:

923

AN XY:

132226

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 SAS exome

AF:

0.0134

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

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00142

Gnomad4 ASJ exome

AF:

0.0112

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0130

Gnomad4 FIN exome

AF:

0.00310

Gnomad4 NFE exome

AF:

0.00858

Gnomad4 OTH exome

AF:

0.00690

GnomAD4 genome

AF:

0.00528

AC:

757

AN:

143320

Hom.:

Cov.:

AF XY:

0.00512

AC XY:

358

AN XY:

69990

show subpopulations

Gnomad4 AFR

AF:

0.00151

Gnomad4 AMR

AF:

0.00143

Gnomad4 ASJ

AF:

0.00764

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.00212

Gnomad4 NFE

AF:

0.00861

Gnomad4 OTH

AF:

0.00639

Alfa

AF:

0.00836

Hom.:

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

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

PrimateAI

Benign

0.22

Polyphen

1.0

D;D

ClinPred

0.092

GERP RS

3.3

Varity_R

0.70

gMVP

0.64

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over