rs2298501
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000528900.5(RDX):c.*388C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,962 control chromosomes in the GnomAD database, including 11,648 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 0.39 ( 11648 hom., cov: 32)
Exomes 𝑓: 0.083 ( 0 hom. )
Consequence
RDX
ENST00000528900.5 3_prime_UTR
ENST00000528900.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.489
Genes affected
RDX (HGNC:9944): (radixin) Radixin is a cytoskeletal protein that may be important in linking actin to the plasma membrane. It is highly similar in sequence to both ezrin and moesin. The radixin gene has been localized by fluorescence in situ hybridization to 11q23. A truncated version representing a pseudogene (RDXP2) was assigned to Xp21.3. Another pseudogene that seemed to lack introns (RDXP1) was mapped to 11p by Southern and PCR analyses. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
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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=-0.75).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDX | NM_001260492.2 | c.*388C>T | 3_prime_UTR_variant | 16/16 | |||
RDX | NM_001260495.2 | c.*388C>T | 3_prime_UTR_variant | 9/9 | |||
RDX | NM_001260496.2 | c.*388C>T | 3_prime_UTR_variant | 8/8 | |||
RDX | NM_001260493.2 | c.*31+3772C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDX | ENST00000528900.5 | c.*388C>T | 3_prime_UTR_variant | 9/9 | 1 | ||||
RDX | ENST00000530301.5 | c.*388C>T | 3_prime_UTR_variant | 8/8 | 1 | ||||
RDX | ENST00000528498.5 | c.*31+3772C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.388 AC: 58846AN: 151830Hom.: 11642 Cov.: 32
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GnomAD4 exome AF: 0.0833 AC: 1AN: 12Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1AN XY: 8
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GnomAD4 genome ? AF: 0.388 AC: 58892AN: 151950Hom.: 11648 Cov.: 32 AF XY: 0.388 AC XY: 28833AN XY: 74262
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at