Variant rs61818749 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001004475.1(OR10T2):c.293G>A(p.Cys98Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,613,750 control chromosomes in the GnomAD database, including 9,214 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 0.080 ( 628 hom., cov: 33)

Exomes 𝑓: 0.10 ( 8586 hom. )

Consequence

OR10T2
NM_001004475.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.45

Variant links:

Genes affected

OR10T2 (HGNC:14816): (olfactory receptor family 10 subfamily T 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]

OR10T2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017620325).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR10T2	NM_001004475.1 linkuse as main transcript	c.293G>A	p.Cys98Tyr	missense_variant	1/1	ENST00000334438.1	NP_001004475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR10T2	ENST00000334438.1 linkuse as main transcript	c.293G>A	p.Cys98Tyr	missense_variant	1/1		NM_001004475.1	ENSP00000334115	P1

Frequencies

GnomAD3 genomes

AF:

0.0803

AC:

12218

AN:

152136

Hom.:

630

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0195

Gnomad AMI

AF:

0.0901

Gnomad AMR

AF:

0.0845

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0881

GnomAD3 exomes

AF:

0.0994

AC:

24916

AN:

250728

Hom.:

1495

AF XY:

0.107

AC XY:

14466

AN XY:

135468

show subpopulations

Gnomad AFR exome

AF:

0.0184

Gnomad AMR exome

AF:

0.0602

Gnomad ASJ exome

AF:

0.0486

Gnomad EAS exome

AF:

0.126

Gnomad SAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.0994

Gnomad OTH exome

AF:

0.0996

GnomAD4 exome

AF:

0.103

AC:

150266

AN:

1461496

Hom.:

8586

Cov.:

AF XY:

0.106

AC XY:

76931

AN XY:

727070

show subpopulations

Gnomad4 AFR exome

AF:

0.0148

Gnomad4 AMR exome

AF:

0.0637

Gnomad4 ASJ exome

AF:

0.0473

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.184

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.100

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.0802

AC:

12210

AN:

152254

Hom.:

628

Cov.:

AF XY:

0.0821

AC XY:

6111

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0194

Gnomad4 AMR

AF:

0.0842

Gnomad4 ASJ

AF:

0.0490

Gnomad4 EAS

AF:

0.132

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.102

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.0867

Alfa

AF:

0.0970

Hom.:

1205

Bravo

AF:

0.0736

TwinsUK

AF:

0.102

AC:

378

ALSPAC

AF:

0.0976

AC:

376

ESP6500AA

AF:

0.0238

AC:

105

ESP6500EA

AF:

0.0995

AC:

856

ExAC

AF:

0.100

AC:

12168

Asia WGS

AF:

0.137

AC:

473

AN:

3478

EpiCase

AF:

0.110

EpiControl

AF:

0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.81

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.28

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.070

Eigen

Pathogenic

0.88

Eigen_PC

Pathogenic

0.72

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.86

MetaRNN

Benign

0.0018

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.8

MutationTaster

Benign

0.00039

PrimateAI

Benign

0.33

PROVEAN

Pathogenic

-11

REVEL

Uncertain

0.31

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.28

MPC

0.017

ClinPred

0.10

GERP RS

4.6

Varity_R

0.94

gMVP

0.40

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

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