rs886038647
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
NM_001365276.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00400
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]
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 | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.10928-16C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000644971.2 | |||
TNXB | NM_019105.8 | c.10922-16C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
TNXB | NM_032470.4 | c.215-16C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.10928-16C>T | splice_polypyrimidine_tract_variant, intron_variant | NM_001365276.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 24AN: 55074Hom.: 0 Cov.: 7 FAILED QC
GnomAD3 genomes
?
AF:
AC:
24
AN:
55074
Hom.:
Cov.:
7
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000477 AC: 26AN: 54496Hom.: 0 AF XY: 0.000437 AC XY: 12AN XY: 27482
GnomAD3 exomes
AF:
AC:
26
AN:
54496
Hom.:
AF XY:
AC XY:
12
AN XY:
27482
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000550 AC: 249AN: 452506Hom.: 0 Cov.: 0 AF XY: 0.000522 AC XY: 125AN XY: 239268
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
249
AN:
452506
Hom.:
Cov.:
0
AF XY:
AC XY:
125
AN XY:
239268
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000435 AC: 24AN: 55114Hom.: 0 Cov.: 7 AF XY: 0.000414 AC XY: 10AN XY: 24132
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
24
AN:
55114
Hom.:
Cov.:
7
AF XY:
AC XY:
10
AN XY:
24132
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at