11-109898688-A-C

Variant names:

• chr11-109898688-A-C
• rs2126869
• ENST00000645527.1:n.*792-33969T>G

Variant summary

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

The ENST00000645527.1(RDX):​n.*792-33969T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,052 control chromosomes in the GnomAD database, including 63,738 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 0.91 (63738 hom., cov: 30)
• Consequence: RDX ENST00000645527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 0 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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.*792-33969T>G		intron_variant	Intron 18 of 18			ENSP00000496121.1
LINC02715	ENST00000692099.1	n.381+58138T>G		intron_variant	Intron 2 of 2
LINC02715	ENST00000818760.1	n.330+58138T>G		intron_variant	Intron 2 of 9

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137574 AN: 151934 Hom.: 63718 Cov.: 30

Gnomad AFR AF: 0.681

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.905 AC: 137647 AN: 152052 Hom.: 63738 Cov.: 30 AF XY: 0.908 AC XY: 67515 AN XY: 74328

African (AFR) AF: 0.681 AC: 28215 AN: 41404

American (AMR) AF: 0.962 AC: 14708 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3464 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4902 AN: 5178

South Asian (SAS) AF: 0.996 AC: 4805 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10594 AN: 10594

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67845 AN: 67976

Other (OTH) AF: 0.909 AC: 1920 AN: 2112

Alfa AF: 0.976 Hom.: 75426

Bravo AF: 0.893

Asia WGS AF: 0.954 AC: 3317 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.84
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2126869; hg19: chr11-109769414;