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1-248453556-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001004136.2(OR2T2):c.759C>T(p.Tyr253=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000748 in 147,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000075 ( 0 hom., cov: 27)
Exomes 𝑓: 0.000051 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR2T2
NM_001004136.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.51
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-248453556-C-T is Benign according to our data. Variant chr1-248453556-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640255.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.51 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR2T2NM_001004136.2 linkuse as main transcriptc.759C>T p.Tyr253= synonymous_variant 4/4 ENST00000641925.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR2T2ENST00000641925.2 linkuse as main transcriptc.759C>T p.Tyr253= synonymous_variant 4/4 NM_001004136.2 P1
OR2T2ENST00000642130.1 linkuse as main transcriptc.759C>T p.Tyr253= synonymous_variant 3/3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000749
AC:
11
AN:
146898
Hom.:
0
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.0000758
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000139
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000236
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000746
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000101
AC:
22
AN:
217000
Hom.:
0
AF XY:
0.0000852
AC XY:
10
AN XY:
117358
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000201
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000650
Gnomad SAS exome
AF:
0.000110
Gnomad FIN exome
AF:
0.0000523
Gnomad NFE exome
AF:
0.000103
Gnomad OTH exome
AF:
0.000182
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000510
AC:
72
AN:
1411700
Hom.:
0
Cov.:
31
AF XY:
0.0000540
AC XY:
38
AN XY:
703396
show subpopulations
Gnomad4 AFR exome
AF:
0.0000309
Gnomad4 AMR exome
AF:
0.000142
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000261
Gnomad4 SAS exome
AF:
0.0000975
Gnomad4 FIN exome
AF:
0.0000571
Gnomad4 NFE exome
AF:
0.0000465
Gnomad4 OTH exome
AF:
0.0000513
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000748
AC:
11
AN:
147010
Hom.:
0
Cov.:
27
AF XY:
0.000126
AC XY:
9
AN XY:
71530
show subpopulations
Gnomad4 AFR
AF:
0.0000756
Gnomad4 AMR
AF:
0.000139
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000236
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000746
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000480
Hom.:
0

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2022OR2T2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
Cadd
Benign
5.9
Dann
Benign
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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.

Other links and lift over

dbSNP: rs763553843; hg19: chr1-248616857; COSMIC: COSV61618280; API