rs7495128
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_134261.3(RORA):c.166+247022G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,100 control chromosomes in the GnomAD database, including 5,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5046 hom., cov: 33)
Consequence
RORA
NM_134261.3 intron
NM_134261.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0860
Publications
3 publications found
Genes affected
RORA (HGNC:10258): (RAR related orphan receptor A) The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It 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, as well as with NM23-1, the product of a tumor metastasis suppressor candidate gene. Also, it has been shown to aid in the transcriptional regulation of some genes involved in circadian rhythm. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2014]
RORA Gene-Disease associations (from GenCC):
- intellectual developmental disorder with or without epilepsy or cerebellar ataxiaInheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.252 AC: 38373AN: 151982Hom.: 5036 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
38373
AN:
151982
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.253 AC: 38411AN: 152100Hom.: 5046 Cov.: 33 AF XY: 0.257 AC XY: 19139AN XY: 74356 show subpopulations
GnomAD4 genome
AF:
AC:
38411
AN:
152100
Hom.:
Cov.:
33
AF XY:
AC XY:
19139
AN XY:
74356
show subpopulations
African (AFR)
AF:
AC:
11995
AN:
41464
American (AMR)
AF:
AC:
3693
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
679
AN:
3470
East Asian (EAS)
AF:
AC:
1723
AN:
5182
South Asian (SAS)
AF:
AC:
1574
AN:
4826
European-Finnish (FIN)
AF:
AC:
3294
AN:
10560
Middle Eastern (MID)
AF:
AC:
53
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14752
AN:
67994
Other (OTH)
AF:
AC:
506
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1510
3019
4529
6038
7548
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1172
AN:
3478
ClinVar
Not reported inComputational 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
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