Variant 1-248453367-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001004136.2(OR2T2):c.570C>T(p.Cys190=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 0 hom., cov: 27)

Exomes 𝑓: 0.0082 ( 40 hom. )

Failed GnomAD Quality Control

Consequence

OR2T2
NM_001004136.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.232

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 -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-248453367-C-T is Benign according to our data. Variant chr1-248453367-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640254.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.232 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2T2	NM_001004136.2 linkuse as main transcript	c.570C>T	p.Cys190=	synonymous_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.570C>T	p.Cys190=	synonymous_variant	4/4		NM_001004136.2	P1
OR2T2	ENST00000642130.1 linkuse as main transcript	c.570C>T	p.Cys190=	synonymous_variant	3/3			P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

800

AN:

148538

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00130

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00309

Gnomad ASJ

AF:

0.00290

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000700

Gnomad FIN

AF:

0.00502

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00911

Gnomad OTH

AF:

0.00585

GnomAD3 exomes

AF:

0.00586

AC:

1398

AN:

238712

Hom.:

AF XY:

0.00589

AC XY:

762

AN XY:

129292

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00287

Gnomad ASJ exome

AF:

0.00163

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000446

Gnomad FIN exome

AF:

0.00586

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.00530

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00820

AC:

11645

AN:

1419778

Hom.:

Cov.:

AF XY:

0.00795

AC XY:

5626

AN XY:

707774

show subpopulations

Gnomad4 AFR exome

AF:

0.00103

Gnomad4 AMR exome

AF:

0.00299

Gnomad4 ASJ exome

AF:

0.00280

Gnomad4 EAS exome

AF:

0.0000260

Gnomad4 SAS exome

AF:

0.000449

Gnomad4 FIN exome

AF:

0.00618

Gnomad4 NFE exome

AF:

0.00979

Gnomad4 OTH exome

AF:

0.00760

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00538

AC:

799

AN:

148644

Hom.:

Cov.:

AF XY:

0.00526

AC XY:

381

AN XY:

72386

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00309

Gnomad4 ASJ

AF:

0.00290

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000701

Gnomad4 FIN

AF:

0.00502

Gnomad4 NFE

AF:

0.00910

Gnomad4 OTH

AF:

0.00579

Alfa

AF:

0.00679

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

OR2T2: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.1

DANN

Benign

0.33

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