chr9-134337481-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002957.6(RXRA):c.28+10822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,082 control chromosomes in the GnomAD database, including 2,560 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 0.18 ( 2560 hom., cov: 33)
Consequence
RXRA
NM_002957.6 intron
NM_002957.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00600
Publications
15 publications found
Genes affected
RXRA (HGNC:10477): (retinoid X receptor alpha) Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.180 AC: 27411AN: 151962Hom.: 2557 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
27411
AN:
151962
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: 0.180 AC: 27436AN: 152082Hom.: 2560 Cov.: 33 AF XY: 0.179 AC XY: 13334AN XY: 74332 show subpopulations
GnomAD4 genome
AF:
AC:
27436
AN:
152082
Hom.:
Cov.:
33
AF XY:
AC XY:
13334
AN XY:
74332
show subpopulations
African (AFR)
AF:
AC:
8309
AN:
41476
American (AMR)
AF:
AC:
2436
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
635
AN:
3472
East Asian (EAS)
AF:
AC:
477
AN:
5152
South Asian (SAS)
AF:
AC:
944
AN:
4824
European-Finnish (FIN)
AF:
AC:
2122
AN:
10584
Middle Eastern (MID)
AF:
AC:
67
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11895
AN:
67972
Other (OTH)
AF:
AC:
394
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1173
2347
3520
4694
5867
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
294
588
882
1176
1470
<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:
537
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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