chr22-19759964-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000332710.8(TBX1):c.34+287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 152,348 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 24 hom., cov: 33)
Consequence
TBX1
ENST00000332710.8 intron
ENST00000332710.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0500
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 22-19759964-G-A is Benign according to our data. Variant chr22-19759964-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1196348.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0113 (1728/152348) while in subpopulation SAS AF= 0.039 (188/4824). AF 95% confidence interval is 0.0344. There are 24 homozygotes in gnomad4. There are 900 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1728 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX1 | NM_005992.1 | c.34+287G>A | intron_variant | ||||
TBX1 | NM_080646.2 | c.34+287G>A | intron_variant | ||||
TBX1 | NM_080647.1 | c.34+287G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000329705.11 | c.34+287G>A | intron_variant | 1 | A2 | ||||
TBX1 | ENST00000332710.8 | c.34+287G>A | intron_variant | 1 | P2 | ||||
TBX1 | ENST00000359500.7 | c.34+287G>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1728AN: 152230Hom.: 24 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: 0.0113 AC: 1728AN: 152348Hom.: 24 Cov.: 33 AF XY: 0.0121 AC XY: 900AN XY: 74508
GnomAD4 genome
?
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3478
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 | Aug 10, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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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