chr15-60502450-C-T
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.1183+310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,114 control chromosomes in the GnomAD database, including 52,858 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 0.82 ( 52858 hom., cov: 31)
Consequence
RORA
NM_134261.3 intron
NM_134261.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.544
Publications
8 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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.823 AC: 125078AN: 151996Hom.: 52821 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
125078
AN:
151996
Hom.:
Cov.:
31
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: 0.823 AC: 125166AN: 152114Hom.: 52858 Cov.: 31 AF XY: 0.827 AC XY: 61511AN XY: 74378 show subpopulations
GnomAD4 genome
AF:
AC:
125166
AN:
152114
Hom.:
Cov.:
31
AF XY:
AC XY:
61511
AN XY:
74378
show subpopulations
African (AFR)
AF:
AC:
25346
AN:
41428
American (AMR)
AF:
AC:
13208
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
3041
AN:
3472
East Asian (EAS)
AF:
AC:
4928
AN:
5188
South Asian (SAS)
AF:
AC:
4522
AN:
4820
European-Finnish (FIN)
AF:
AC:
9769
AN:
10602
Middle Eastern (MID)
AF:
AC:
239
AN:
294
European-Non Finnish (NFE)
AF:
AC:
61555
AN:
68002
Other (OTH)
AF:
AC:
1759
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
986
1971
2957
3942
4928
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
872
1744
2616
3488
4360
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3216
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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