rs2234753
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002957.6(RXRA):c.279+33G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,515,030 control chromosomes in the GnomAD database, including 445,516 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 0.80 ( 48457 hom., cov: 31)
Exomes 𝑓: 0.76 ( 397059 hom. )
Consequence
RXRA
NM_002957.6 intron
NM_002957.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.334
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.279+33G>A | intron_variant | ENST00000481739.2 | |||
RXRA | NM_001291920.2 | c.198+33G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.279+33G>A | intron_variant | 1 | NM_002957.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.795 AC: 120769AN: 151882Hom.: 48415 Cov.: 31
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GnomAD3 exomes AF: 0.773 AC: 140973AN: 182344Hom.: 54304 AF XY: 0.768 AC XY: 76892AN XY: 100130
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GnomAD4 exome AF: 0.761 AC: 1037849AN: 1363032Hom.: 397059 Cov.: 24 AF XY: 0.757 AC XY: 509389AN XY: 673320
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GnomAD4 genome ? AF: 0.795 AC: 120864AN: 151998Hom.: 48457 Cov.: 31 AF XY: 0.792 AC XY: 58802AN XY: 74286
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at