ENST00000645527.1:n.*758-44683C>T

Variant names:

• chr11-110035472-G-A
• rs1789374
• ENST00000645527.1:n.*758-44683C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645527.1(RDX):​n.*758-44683C>T variant causes a intron 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: RDX ENST00000645527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 1 publications found

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]

LINC02715 (HGNC:54232): (long intergenic non-protein coding RNA 2715)

ENSG00000306553 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RDX	ENST00000645527.1	n.*758-44683C>T		intron_variant	Intron 17 of 18			ENSP00000496121.1
LINC02715	ENST00000692099.1	n.320+52382C>T		intron_variant	Intron 1 of 2
LINC02715	ENST00000819036.1	n.320+52382C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.868 AC: 36022 AN: 41506

American (AMR) AF: 0.695 AC: 10619 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3468

East Asian (EAS) AF: 0.829 AC: 4295 AN: 5184

South Asian (SAS) AF: 0.725 AC: 3486 AN: 4808

European-Finnish (FIN) AF: 0.686 AC: 7238 AN: 10558

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47172 AN: 67978

Other (OTH) AF: 0.741 AC: 1563 AN: 2108

Alfa AF: 0.712 Hom.: 163779

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1789374; hg19: chr11-109906198;