chr6-32044149-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001365276.2(TNXB):c.11264-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 1,471,384 control chromosomes in the GnomAD database, including 548 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 56 hom., cov: 19)
Exomes 𝑓: 0.019 ( 492 hom. )
Consequence
TNXB
NM_001365276.2 intron
NM_001365276.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.64
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 6-32044149-C-T is Benign according to our data. Variant chr6-32044149-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 261104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0162 (2150/132592) while in subpopulation NFE AF= 0.0235 (1443/61452). AF 95% confidence interval is 0.0225. There are 56 homozygotes in gnomad4. There are 1059 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 56 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.11264-20G>A | intron_variant | ENST00000644971.2 | NP_001352205.1 | |||
TNXB | NM_019105.8 | c.11258-20G>A | intron_variant | NP_061978.6 | ||||
TNXB | NM_032470.4 | c.551-20G>A | intron_variant | NP_115859.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.11264-20G>A | intron_variant | NM_001365276.2 | ENSP00000496448 |
Frequencies
GnomAD3 genomes AF: 0.0163 AC: 2155AN: 132510Hom.: 57 Cov.: 19
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GnomAD3 exomes AF: 0.0185 AC: 3726AN: 201420Hom.: 108 AF XY: 0.0187 AC XY: 2039AN XY: 109078
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GnomAD4 exome AF: 0.0192 AC: 25760AN: 1338792Hom.: 492 Cov.: 31 AF XY: 0.0192 AC XY: 12779AN XY: 665472
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GnomAD4 genome AF: 0.0162 AC: 2150AN: 132592Hom.: 56 Cov.: 19 AF XY: 0.0165 AC XY: 1059AN XY: 64068
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
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 | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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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