Variant chr1-248453107-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001004136.2(OR2T2):c.310C>T(p.Leu104Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 1,366,624 control chromosomes in the GnomAD database, including 4,140 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 1187 hom., cov: 32)

Exomes 𝑓: 0.050 ( 2953 hom. )

Consequence

OR2T2
NM_001004136.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.06

Variant links:

Genes affected

OR2T2 (HGNC:14725): (olfactory receptor family 2 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]

OR2T2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.804666E-4).

BP6

Variant 1-248453107-C-T is Benign according to our data. Variant chr1-248453107-C-T is described in ClinVar as [Benign]. Clinvar id is 767777.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2T2	NM_001004136.2 linkuse as main transcript	c.310C>T	p.Leu104Phe	missense_variant	4/4	ENST00000641925.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2T2	ENST00000641925.2 linkuse as main transcript	c.310C>T	p.Leu104Phe	missense_variant	4/4		NM_001004136.2	P1
OR2T2	ENST00000642130.1 linkuse as main transcript	c.310C>T	p.Leu104Phe	missense_variant	3/3			P1

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

22608

AN:

110784

Hom.:

1184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.0429

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.0889

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.0772

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.144

GnomAD4 exome

AF:

0.0501

AC:

62906

AN:

1255752

Hom.:

2953

Cov.:

AF XY:

0.0538

AC XY:

33373

AN XY:

620166

show subpopulations

Gnomad4 AFR exome

AF:

0.261

Gnomad4 AMR exome

AF:

0.0873

Gnomad4 ASJ exome

AF:

0.0563

Gnomad4 EAS exome

AF:

0.187

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.0295

Gnomad4 OTH exome

AF:

0.0667

GnomAD4 genome

AF:

0.204

AC:

22645

AN:

110872

Hom.:

1187

Cov.:

AF XY:

0.205

AC XY:

11073

AN XY:

54096

show subpopulations

Gnomad4 AFR

AF:

0.424

Gnomad4 AMR

AF:

0.147

Gnomad4 ASJ

AF:

0.0889

Gnomad4 EAS

AF:

0.211

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.100

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.275

Hom.:

116

ExAC

AF:

0.327

AC:

39736

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 02, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.11

DEOGEN2

Benign

0.0097

T;T;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.015

MetaRNN

Benign

0.00098

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.63

N;N;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.15

.;.;N

REVEL

Benign

0.014

Sift

Benign

0.56

.;.;T

Sift4G

Benign

0.93

.;.;T

Polyphen

0.0080

B;B;B

Vest4

0.059

MPC

1.6

ClinPred

0.0075

GERP RS

-0.64

Varity_R

0.036

gMVP

0.10

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over