Variant chrX-9687887-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_005647.4(TBL1X):c.358-130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.79 ( 25260 hom., 24980 hem., cov: 21)

Exomes 𝑓: 0.89 ( 267899 hom. 268753 hem. )

Failed GnomAD Quality Control

Consequence

TBL1X
NM_005647.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.156

Variant links:

Genes affected

TBL1X (HGNC:11585): (transducin beta like 1 X-linked) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This encoded protein is found as a subunit in corepressor SMRT (silencing mediator for retinoid and thyroid receptors) complex along with histone deacetylase 3 protein. This gene is located adjacent to the ocular albinism gene and it is thought to be involved in the pathogenesis of the ocular albinism with late-onset sensorineural deafness phenotype. Four transcript variants encoding two different isoforms have been found for this gene. This gene is highly similar to the Y chromosome TBL1Y gene. [provided by RefSeq, Nov 2008]

TBL1X links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant X-9687887-G-A is Benign according to our data. Variant chrX-9687887-G-A is described in ClinVar as [Benign]. Clinvar id is 1221121.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
TBL1X	NM_005647.4 linkuse as main transcript	c.358-130G>A	intron_variant	ENST00000645353.2
TBL1X	NM_001139466.1 linkuse as main transcript	c.358-130G>A	intron_variant
TBL1X	NM_001139467.1 linkuse as main transcript	c.205-130G>A	intron_variant
TBL1X	NM_001139468.1 linkuse as main transcript	c.205-130G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBL1X	ENST00000645353.2 linkuse as main transcript	c.358-130G>A		intron_variant			NM_005647.4		O60907-1

Frequencies

GnomAD3 genomes

AF:

0.792

AC:

86164

AN:

108754

Hom.:

25261

Cov.:

AF XY:

0.801

AC XY:

24946

AN XY:

31162

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.831

Gnomad AMR

AF:

0.889

Gnomad ASJ

AF:

0.841

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.953

Gnomad FIN

AF:

0.875

Gnomad MID

AF:

0.833

Gnomad NFE

AF:

0.892

Gnomad OTH

AF:

0.802

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.894

AC:

866349

AN:

969320

Hom.:

267899

AF XY:

0.898

AC XY:

268753

AN XY:

299234

show subpopulations

Gnomad4 AFR exome

AF:

0.518

Gnomad4 AMR exome

AF:

0.915

Gnomad4 ASJ exome

AF:

0.850

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.955

Gnomad4 FIN exome

AF:

0.879

Gnomad4 NFE exome

AF:

0.900

Gnomad4 OTH exome

AF:

0.879

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.792

AC:

86193

AN:

108805

Hom.:

25260

Cov.:

AF XY:

0.800

AC XY:

24980

AN XY:

31223

show subpopulations

Gnomad4 AFR

AF:

0.526

Gnomad4 AMR

AF:

0.889

Gnomad4 ASJ

AF:

0.841

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.954

Gnomad4 FIN

AF:

0.875

Gnomad4 NFE

AF:

0.892

Gnomad4 OTH

AF:

0.805

Alfa

AF:

0.798

Hom.:

5341

Bravo

AF:

0.781

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.4

DANN

Benign

0.43

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over