6-32042509-G-C
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001365276.2(TNXB):c.12156C>G(p.Arg4052=) variant causes a synonymous 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 0.0039 ( 0 hom., cov: 20)
Exomes 𝑓: 0.0013 ( 13 hom. )
Failed GnomAD Quality Control
Consequence
TNXB
NM_001365276.2 synonymous
NM_001365276.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.94
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 6-32042509-G-C is Benign according to our data. Variant chr6-32042509-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 261119.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-3.94 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 8 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.12156C>G | p.Arg4052= | synonymous_variant | 40/44 | ENST00000644971.2 | |
TNXB | NM_019105.8 | c.12150C>G | p.Arg4050= | synonymous_variant | 40/44 | ||
TNXB | NM_032470.4 | c.1443C>G | p.Arg481= | synonymous_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.12156C>G | p.Arg4052= | synonymous_variant | 40/44 | NM_001365276.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00396 AC: 596AN: 150556Hom.: 0 Cov.: 20
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GnomAD3 exomes AF: 0.00166 AC: 408AN: 245372Hom.: 8 AF XY: 0.00184 AC XY: 245AN XY: 132886
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00128 AC: 1850AN: 1441036Hom.: 13 Cov.: 33 AF XY: 0.00145 AC XY: 1037AN XY: 716456
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.00394 AC: 593AN: 150684Hom.: 0 Cov.: 20 AF XY: 0.00405 AC XY: 298AN XY: 73636
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Ehlers-Danlos syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Dec 01, 2019 | - - |
Ehlers-Danlos syndrome due to tenascin-X deficiency;C4014831:Vesicoureteral reflux 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 01, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at