11-110237567-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_002906.4(RDX):c.1176G>A(p.Glu392Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

RDX
NM_002906.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.282

Publications

1 publications found

Variant links:

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]

RDX Gene-Disease associations (from GenCC):

nonsyndromic genetic hearing loss
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
autosomal recessive nonsyndromic hearing loss 24
Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)
hearing loss, autosomal recessive
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

RDX links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 11-110237567-C-T is Benign according to our data. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-110237567-C-T is described in CliVar as Likely_benign. Clinvar id is 180030.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.282 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDX	NM_002906.4 link	c.1176G>A	p.Glu392Glu	synonymous_variant	Exon 11 of 14	ENST00000645495.2	NP_002897.1	P35241-1B0YJ88Q6PKD3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RDX	ENST00000645495.2 link	c.1176G>A	p.Glu392Glu	synonymous_variant	Exon 11 of 14		NM_002906.4	ENSP00000496503.2		P35241-1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000398

AC:

AN:

251456

AF XY:

0.00000736

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461786

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727198

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39698

South Asian (SAS)

AF:

0.0000116

AC:

AN:

86250

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5684

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1112008

Other (OTH)

AF:

0.00

AC:

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152188

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41442

American (AMR)

AF:

0.00

AC:

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5200

South Asian (SAS)

AF:

0.000207

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68036

Other (OTH)

AF:

0.00

AC:

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Sep 16, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Glu392Glu in exon 11 of RDX: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

6.2

(source)

DANN

Benign

0.43

PhyloP100

-0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over