rs373531814
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365276.2(TNXB):c.9440-48G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000662 in 1,577,484 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00069 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00066 ( 16 hom. )
Consequence
TNXB
NM_001365276.2 intron
NM_001365276.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.109
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 6-32049635-C-A is Benign according to our data. Variant chr6-32049635-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 261177.Status of the report is criteria_provided_single_submitter, 1 stars.
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.9440-48G>T | intron_variant | ENST00000644971.2 | |||
TNXB | NM_019105.8 | c.9434-48G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.9440-48G>T | intron_variant | NM_001365276.2 | |||||
TNXB | ENST00000375244.7 | c.9440-48G>T | intron_variant | 5 | |||||
TNXB | ENST00000647633.1 | c.10181-48G>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000691 AC: 105AN: 151992Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00130 AC: 282AN: 217228Hom.: 6 AF XY: 0.00127 AC XY: 152AN XY: 119450
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GnomAD4 exome AF: 0.000659 AC: 939AN: 1425374Hom.: 16 Cov.: 32 AF XY: 0.000673 AC XY: 475AN XY: 705702
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GnomAD4 genome ? AF: 0.000690 AC: 105AN: 152110Hom.: 2 Cov.: 32 AF XY: 0.000753 AC XY: 56AN XY: 74352
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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
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Name
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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