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GeneBe

1-247451461-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001004492.2(OR2B11):c.522G>A(p.Gly174=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00516 in 1,614,130 control chromosomes in the GnomAD database, including 397 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 201 hom., cov: 33)
Exomes 𝑓: 0.0029 ( 196 hom. )

Consequence

OR2B11
NM_001004492.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.42
Variant links:
Genes affected
OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

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=-0.82).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-247451461-C-T is Benign according to our data. Variant chr1-247451461-C-T is described in ClinVar as [Benign]. Clinvar id is 775699.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=-2.42 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0916 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR2B11NM_001004492.2 linkuse as main transcriptc.522G>A p.Gly174= synonymous_variant 2/2 ENST00000641149.2
OR2B11NR_169840.1 linkuse as main transcriptn.1176G>A non_coding_transcript_exon_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR2B11ENST00000641149.2 linkuse as main transcriptc.522G>A p.Gly174= synonymous_variant 2/2 NM_001004492.2 P1
OR2B11ENST00000641527.1 linkuse as main transcriptc.522G>A p.Gly174= synonymous_variant 3/3 P1
OR2B11ENST00000641613.1 linkuse as main transcriptn.1176G>A non_coding_transcript_exon_variant 5/5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0268
AC:
4078
AN:
152184
Hom.:
199
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0940
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00824
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000279
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00710
AC:
1783
AN:
251094
Hom.:
87
AF XY:
0.00518
AC XY:
703
AN XY:
135760
show subpopulations
Gnomad AFR exome
AF:
0.0942
Gnomad AMR exome
AF:
0.00451
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00160
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000255
Gnomad OTH exome
AF:
0.00375
GnomAD4 exome
AF:
0.00290
AC:
4242
AN:
1461828
Hom.:
196
Cov.:
71
AF XY:
0.00253
AC XY:
1839
AN XY:
727216
show subpopulations
Gnomad4 AFR exome
AF:
0.0969
Gnomad4 AMR exome
AF:
0.00517
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.00158
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000190
Gnomad4 OTH exome
AF:
0.00641
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0269
AC:
4094
AN:
152302
Hom.:
201
Cov.:
33
AF XY:
0.0260
AC XY:
1940
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0941
Gnomad4 AMR
AF:
0.00823
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000279
Gnomad4 OTH
AF:
0.0133
Alfa
AF:
0.0159
Hom.:
53
Bravo
AF:
0.0308
Asia WGS
AF:
0.00779
AC:
27
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000415

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
9.9
Dann
Benign
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.15
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: rs58058243; hg19: chr1-247614763; API