Variant rs2734313 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001365276.2(TNXB):c.11650+10C>G 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 0.42 ( 4178 hom., cov: 7)

Exomes 𝑓: 0.45 ( 50170 hom. )

Consequence

TNXB
NM_001365276.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

TNXB (HGNC:11976): (tenascin XB) This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The tenascins have anti-adhesive effects, as opposed to fibronectin which is adhesive. This protein is thought to function in matrix maturation during wound healing, and its deficiency has been associated with the connective tissue disorder Ehlers-Danlos syndrome. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. It is one of four genes in this cluster which have been duplicated. The duplicated copy of this gene is incomplete and is a pseudogene which is transcribed but does not encode a protein. The structure of this gene is unusual in that it overlaps the CREBL1 and CYP21A2 genes at its 5' and 3' ends, respectively. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

TNXB links:

TNXB (HGNC:):

TNXB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 6-32043427-G-C is Benign according to our data. Variant chr6-32043427-G-C is described in ClinVar as [Benign]. Clinvar id is 261115.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-32043427-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TNXB	NM_001365276.2 linkuse as main transcript	c.11650+10C>G	intron_variant	ENST00000644971.2	NP_001352205.1
TNXB	NM_019105.8 linkuse as main transcript	c.11644+10C>G	intron_variant		NP_061978.6	P22105-1O95680Q9Y464O95681
TNXB	NM_032470.4 linkuse as main transcript	c.937+10C>G	intron_variant		NP_115859.2	P22105-2Q6IPK3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNXB	ENST00000644971.2 linkuse as main transcript	c.11650+10C>G		intron_variant			NM_001365276.2	ENSP00000496448.1		P22105-3

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

17749

AN:

41826

Hom.:

4176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.574

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.405

Gnomad OTH

AF:

0.446

GnomAD3 exomes

AF:

0.464

AC:

35360

AN:

76204

Hom.:

8636

AF XY:

0.450

AC XY:

17585

AN XY:

39044

show subpopulations

Gnomad AFR exome

AF:

0.472

Gnomad AMR exome

AF:

0.589

Gnomad ASJ exome

AF:

0.563

Gnomad EAS exome

AF:

0.392

Gnomad SAS exome

AF:

0.379

Gnomad FIN exome

AF:

0.394

Gnomad NFE exome

AF:

0.430

Gnomad OTH exome

AF:

0.442

GnomAD4 exome

AF:

0.453

AC:

216796

AN:

478920

Hom.:

50170

Cov.:

AF XY:

0.450

AC XY:

113597

AN XY:

252172

show subpopulations

Gnomad4 AFR exome

AF:

0.466

Gnomad4 AMR exome

AF:

0.575

Gnomad4 ASJ exome

AF:

0.571

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.402

Gnomad4 FIN exome

AF:

0.445

Gnomad4 NFE exome

AF:

0.444

Gnomad4 OTH exome

AF:

0.449

GnomAD4 genome

AF:

0.424

AC:

17758

AN:

41862

Hom.:

4178

Cov.:

AF XY:

0.425

AC XY:

7617

AN XY:

17932

show subpopulations

Gnomad4 AFR

AF:

0.430

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.539

Gnomad4 EAS

AF:

0.382

Gnomad4 SAS

AF:

0.396

Gnomad4 FIN

AF:

0.434

Gnomad4 NFE

AF:

0.405

Gnomad4 OTH

AF:

0.445

Alfa

AF:

0.445

Hom.:

1916

Bravo

AF:

0.466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 10, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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