rs2856450
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001365276.2(TNXB):c.11264-48A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000584 in 1,317,606 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000066 ( 2 hom., cov: 18)
Exomes 𝑓: 0.000058 ( 6 hom. )
Consequence
TNXB
NM_001365276.2 intron
NM_001365276.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BS2
?
High Homozygotes in GnomAd4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.11264-48A>T | intron_variant | ENST00000644971.2 | |||
TNXB | NM_019105.8 | c.11258-48A>T | intron_variant | ||||
TNXB | NM_032470.4 | c.551-48A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.11264-48A>T | intron_variant | NM_001365276.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 7AN: 106604Hom.: 2 Cov.: 18
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GnomAD3 exomes AF: 0.0000998 AC: 18AN: 180354Hom.: 4 AF XY: 0.000113 AC XY: 11AN XY: 97496
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GnomAD4 exome AF: 0.0000578 AC: 70AN: 1211002Hom.: 6 Cov.: 31 AF XY: 0.0000563 AC XY: 34AN XY: 603852
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GnomAD4 genome ? AF: 0.0000657 AC: 7AN: 106604Hom.: 2 Cov.: 18 AF XY: 0.0000584 AC XY: 3AN XY: 51370
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at