22-19759559-G-TC
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000332710.8(TBX1):c.-85delinsTC variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 36)
Consequence
TBX1
ENST00000332710.8 splice_region, 5_prime_UTR
ENST00000332710.8 splice_region, 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.611
Genes affected
TBX1 (HGNC:11592): (T-box transcription factor 1) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene product shares 98% amino acid sequence identity with the mouse ortholog. DiGeorge syndrome (DGS)/velocardiofacial syndrome (VCFS), a common congenital disorder characterized by neural-crest-related developmental defects, has been associated with deletions of chromosome 22q11.2, where this gene has been mapped. Studies using mouse models of DiGeorge syndrome suggest a major role for this gene in the molecular etiology of DGS/VCFS. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 22-19759559-G-TC is Benign according to our data. Variant chr22-19759559-G-TC is described in ClinVar as [Benign]. Clinvar id is 1220890.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX1 | NM_005992.1 | c.-85delinsTC | splice_region_variant, 5_prime_UTR_variant | 2/10 | |||
TBX1 | NM_080646.2 | c.-85delinsTC | splice_region_variant, 5_prime_UTR_variant | 2/9 | |||
TBX1 | NM_080647.1 | c.-85delinsTC | splice_region_variant, 5_prime_UTR_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000329705.11 | c.-85delinsTC | splice_region_variant, 5_prime_UTR_variant | 2/9 | 1 | A2 | |||
TBX1 | ENST00000332710.8 | c.-85delinsTC | splice_region_variant, 5_prime_UTR_variant | 2/9 | 1 | P2 | |||
TBX1 | ENST00000359500.7 | c.-85delinsTC | splice_region_variant, 5_prime_UTR_variant | 2/10 | 1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 36
GnomAD3 genomes
Cov.:
36
GnomAD4 exome Cov.: 54
GnomAD4 exome
Cov.:
54
GnomAD4 genome Cov.: 36
GnomAD4 genome
Cov.:
36
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.