rs340020
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_134261.3(RORA):c.196+64767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 151,606 control chromosomes in the GnomAD database, including 11 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 0.0069 ( 11 hom., cov: 30)
Consequence
RORA
NM_134261.3 intron
NM_134261.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.27
Publications
1 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]
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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=-0.88).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00689 (1045/151606) while in subpopulation AFR AF = 0.0242 (998/41232). AF 95% confidence interval is 0.023. There are 11 homozygotes in GnomAd4. There are 494 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
BS2
High AC in GnomAd4 at 1045 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00692 AC: 1048AN: 151494Hom.: 11 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
1048
AN:
151494
Hom.:
Cov.:
30
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 0.00689 AC: 1045AN: 151606Hom.: 11 Cov.: 30 AF XY: 0.00667 AC XY: 494AN XY: 74100 show subpopulations
GnomAD4 genome
AF:
AC:
1045
AN:
151606
Hom.:
Cov.:
30
AF XY:
AC XY:
494
AN XY:
74100
show subpopulations
African (AFR)
AF:
AC:
998
AN:
41232
American (AMR)
AF:
AC:
31
AN:
15236
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5158
South Asian (SAS)
AF:
AC:
0
AN:
4800
European-Finnish (FIN)
AF:
AC:
0
AN:
10446
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
5
AN:
67954
Other (OTH)
AF:
AC:
11
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
47
94
140
187
234
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3476
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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