rs2298501

Positions:

• chr11-110195809-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 58846 AN: 151830 Hom.: 11642 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.362

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.388 AC: 58892 AN: 151950 Hom.: 11648 Cov.: 32 AF XY: 0.388 AC XY: 28833 AN XY: 74262

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.365

Alfa AF: 0.394 Hom.: 1483

Bravo AF: 0.379

Asia WGS AF: 0.468 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.4
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2298501; hg19: chr11-110066534;