22-19759960-A-AG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000332710.8(TBX1):c.34+289dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 152,276 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 1 hom., cov: 33)
Consequence
TBX1
ENST00000332710.8 intron
ENST00000332710.8 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.842
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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 22-19759960-A-AG is Benign according to our data. Variant chr22-19759960-A-AG is described in ClinVar as [Likely_benign]. Clinvar id is 1186588.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00317 (483/152276) while in subpopulation AFR AF= 0.0104 (434/41564). AF 95% confidence interval is 0.00963. There are 1 homozygotes in gnomad4. There are 223 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 482 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX1 | NM_005992.1 | c.34+289dup | intron_variant | ||||
TBX1 | NM_080646.2 | c.34+289dup | intron_variant | ||||
TBX1 | NM_080647.1 | c.34+289dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000329705.11 | c.34+289dup | intron_variant | 1 | A2 | ||||
TBX1 | ENST00000332710.8 | c.34+289dup | intron_variant | 1 | P2 | ||||
TBX1 | ENST00000359500.7 | c.34+289dup | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00317 AC: 482AN: 152158Hom.: 1 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00317 AC: 483AN: 152276Hom.: 1 Cov.: 33 AF XY: 0.00300 AC XY: 223AN XY: 74450
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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 | GeneDx | Jan 09, 2020 | - - |
Computational scores
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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