rs1789374

chr11-110035472-G-Achr11-110035472-G-C

Variant summary

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

The ENST00000692099.1(ENSG00000289465):n.320+52382C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,078 control chromosomes in the GnomAD database, including 43,069 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 0.75 (43069 hom., cov: 32)
• Consequence: ENST00000692099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

(HGNC:):

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692099.1	n.320+52382C>T		intron_variant, non_coding_transcript_variant
RDX	ENST00000645527.1	c.*758-44683C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113642 AN: 151960 Hom.: 43021 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.742

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.748 AC: 113754 AN: 152078 Hom.: 43069 Cov.: 32 AF XY: 0.747 AC XY: 55551 AN XY: 74316

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.741

Alfa AF: 0.703 Hom.: 76604

Bravo AF: 0.753

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.5
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789374; hg19: chr11-109906198;