rs11606636

Variant names:

• chr11-109986510-T-C
• rs11606636
• ENST00000645527.1:n.*791+4246A>G

Variant summary

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

The ENST00000645527.1(RDX):​n.*791+4246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,162 control chromosomes in the GnomAD database, including 9,485 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 0.35 (9485 hom., cov: 33)
• Consequence: RDX ENST00000645527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730
• 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)

ENSG00000287245 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 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.*791+4246A>G		intron_variant	Intron 18 of 18			ENSP00000496121.1
LINC02715	ENST00000692099.1	n.321-29624A>G		intron_variant	Intron 1 of 2
LINC02715	ENST00000819036.1	n.321-29624A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53181 AN: 152042 Hom.: 9481 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.350 AC: 53192 AN: 152162 Hom.: 9485 Cov.: 33 AF XY: 0.346 AC XY: 25720 AN XY: 74374

African (AFR) AF: 0.325 AC: 13480 AN: 41506

American (AMR) AF: 0.321 AC: 4909 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1226 AN: 5186

South Asian (SAS) AF: 0.350 AC: 1690 AN: 4830

European-Finnish (FIN) AF: 0.328 AC: 3470 AN: 10582

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 26001 AN: 67988

Other (OTH) AF: 0.344 AC: 727 AN: 2112

Alfa AF: 0.372 Hom.: 7292

Bravo AF: 0.348

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs11606636; hg19: chr11-109857236;