rs375934653
Variant names:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006914.4(RORB):c.42C>T(p.Gly14Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,922 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 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
RORB
NM_006914.4 synonymous
NM_006914.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.528
Publications
1 publications found
Genes affected
RORB (HGNC:10259): (RAR related orphan receptor B) The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It is a DNA-binding protein that can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, and to help regulate the expression of some genes involved in circadian rhythm. [provided by RefSeq, Feb 2014]
RORB Gene-Disease associations (from GenCC):
- epilepsy, idiopathic generalized, susceptibility to, 15Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- complex neurodevelopmental disorderInheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
- epilepsyInheritance: AD Classification: MODERATE Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.2).
BP6
Variant 9-74630316-C-T is Benign according to our data. Variant chr9-74630316-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1947724.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.528 with no splicing effect.
BS2
High AC in GnomAdExome4 at 10 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152064Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
152064
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000279 AC: 7AN: 250878 AF XY: 0.0000369 show subpopulations
GnomAD2 exomes
AF:
AC:
7
AN:
250878
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460858Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726746 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
1460858
Hom.:
Cov.:
32
AF XY:
AC XY:
5
AN XY:
726746
show subpopulations
African (AFR)
AF:
AC:
4
AN:
33446
American (AMR)
AF:
AC:
0
AN:
44668
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26124
East Asian (EAS)
AF:
AC:
1
AN:
39680
South Asian (SAS)
AF:
AC:
0
AN:
86102
European-Finnish (FIN)
AF:
AC:
0
AN:
53402
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1111330
Other (OTH)
AF:
AC:
1
AN:
60340
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.405
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152064Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74254 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
152064
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
74254
show subpopulations
African (AFR)
AF:
AC:
4
AN:
41404
American (AMR)
AF:
AC:
0
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3460
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10588
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68010
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 06, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.