6-32041801-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001365276.2(TNXB):c.12603C>T(p.Asn4201Asn) 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 0.0000078 ( 0 hom., cov: 18)
Exomes 𝑓: 0.000022 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TNXB
NM_001365276.2 synonymous
NM_001365276.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.90
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 -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 6-32041801-G-A is Benign according to our data. Variant chr6-32041801-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1711621.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.9 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.12603C>T | p.Asn4201Asn | synonymous_variant | 43/44 | ENST00000644971.2 | NP_001352205.1 | |
TNXB | NM_001428335.1 | c.13344C>T | p.Asn4448Asn | synonymous_variant | 44/45 | NP_001415264.1 | ||
TNXB | NM_019105.8 | c.12597C>T | p.Asn4199Asn | synonymous_variant | 43/44 | NP_061978.6 | ||
TNXB | NM_032470.4 | c.1890C>T | p.Asn630Asn | synonymous_variant | 12/13 | NP_115859.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000777 AC: 1AN: 128716Hom.: 0 Cov.: 18
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GnomAD3 exomes AF: 0.0000230 AC: 3AN: 130352Hom.: 0 AF XY: 0.0000285 AC XY: 2AN XY: 70100
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000223 AC: 19AN: 853122Hom.: 0 Cov.: 12 AF XY: 0.0000297 AC XY: 13AN XY: 437674
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000777 AC: 1AN: 128716Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 61896
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | TNXB: BP4, BP7 - |
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