Variant chr1-248453100-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001004136.2(OR2T2):c.303G>A(p.Gln101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 1,367,646 control chromosomes in the GnomAD database, including 4,138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 1183 hom., cov: 32)

Exomes 𝑓: 0.050 ( 2955 hom. )

Consequence

OR2T2
NM_001004136.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.291

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-248453100-G-A is Benign according to our data. Variant chr1-248453100-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 767776.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.291 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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.303G>A	p.Gln101=	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.303G>A	p.Gln101=	synonymous_variant	4/4		NM_001004136.2	P1
OR2T2	ENST00000642130.1 linkuse as main transcript	c.303G>A	p.Gln101=	synonymous_variant	3/3			P1

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

22341

AN:

111164

Hom.:

1180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.421

Gnomad AMI

AF:

0.0446

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.0656

Gnomad NFE

AF:

0.0983

Gnomad OTH

AF:

0.140

GnomAD4 exome

AF:

0.0495

AC:

62247

AN:

1256396

Hom.:

2955

Cov.:

AF XY:

0.0532

AC XY:

33010

AN XY:

620420

show subpopulations

Gnomad4 AFR exome

AF:

0.259

Gnomad4 AMR exome

AF:

0.0851

Gnomad4 ASJ exome

AF:

0.0557

Gnomad4 EAS exome

AF:

0.185

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.0291

Gnomad4 OTH exome

AF:

0.0662

GnomAD4 genome

AF:

0.201

AC:

22379

AN:

111250

Hom.:

1183

Cov.:

AF XY:

0.201

AC XY:

10938

AN XY:

54298

show subpopulations

Gnomad4 AFR

AF:

0.421

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.0873

Gnomad4 EAS

AF:

0.208

Gnomad4 SAS

AF:

0.173

Gnomad4 FIN

AF:

0.171

Gnomad4 NFE

AF:

0.0983

Gnomad4 OTH

AF:

0.139

Alfa

AF:

0.273

Hom.:

128

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.3

DANN

Benign

0.50

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