rs11606636

Positions:

• chr11-109986510-T-C

Variant summary

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

The ENST00000692099.1(ENSG00000289465):​n.321-29624A>G 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 0.35 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: ENST00000692099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730

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=-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692099.1	n.321-29624A>G		intron_variant, non_coding_transcript_variant
RDX	ENST00000645527.1	c.*791+4246A>G		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.344

Alfa AF: 0.376 Hom.: 5129

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11606636; hg19: chr11-109857236;