Variant 6-32044732-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_001365276.2(TNXB):c.10928-16C>T variant causes a splice polypyrimidine tract, 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.00044 ( 0 hom., cov: 7)

Exomes 𝑓: 0.00055 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TNXB
NM_001365276.2 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00400

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 6-32044732-G-A is Benign according to our data. Variant chr6-32044732-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 261100.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-32044732-G-A is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
TNXB	NM_001365276.2 linkuse as main transcript	c.10928-16C>T	splice_polypyrimidine_tract_variant, intron_variant	ENST00000644971.2	NP_001352205.1
TNXB	NM_019105.8 linkuse as main transcript	c.10922-16C>T	splice_polypyrimidine_tract_variant, intron_variant		NP_061978.6
TNXB	NM_032470.4 linkuse as main transcript	c.215-16C>T	splice_polypyrimidine_tract_variant, intron_variant		NP_115859.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNXB	ENST00000644971.2 linkuse as main transcript	c.10928-16C>T		splice_polypyrimidine_tract_variant, intron_variant			NM_001365276.2	ENSP00000496448		P22105-3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

55074

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000710

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000677

Gnomad ASJ

AF:

0.000581

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000339

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000691

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000477

AC:

AN:

54496

Hom.:

AF XY:

0.000437

AC XY:

AN XY:

27482

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000838

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000787

Gnomad OTH exome

AF:

0.000520

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000550

AC:

249

AN:

452506

Hom.:

Cov.:

AF XY:

0.000522

AC XY:

125

AN XY:

239268

show subpopulations

Gnomad4 AFR exome

AF:

0.0000791

Gnomad4 AMR exome

AF:

0.000983

Gnomad4 ASJ exome

AF:

0.00151

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000217

Gnomad4 FIN exome

AF:

0.000206

Gnomad4 NFE exome

AF:

0.000701

Gnomad4 OTH exome

AF:

0.000382

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000435

AC:

AN:

55114

Hom.:

Cov.:

AF XY:

0.000414

AC XY:

AN XY:

24132

show subpopulations

Gnomad4 AFR

AF:

0.0000707

Gnomad4 AMR

AF:

0.000675

Gnomad4 ASJ

AF:

0.000581

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000339

Gnomad4 NFE

AF:

0.000692

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.4

DANN

Benign

0.66

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