22-19759510-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BS1 BS2

The ENST00000332710.8(TBX1):c.-86-48C>G variant causes a intron change. The variant allele was found at a frequency of 0.0135 in 1,514,532 control chromosomes in the GnomAD database, including 182 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0079 (11 hom., cov: 35)
  • Exomes 𝑓: 0.014 (171 hom.)
• Consequence: TBX1 ENST00000332710.8 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.22

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BP6: Variant 22-19759510-C-G is Benign according to our data. Variant chr22-19759510-C-G is described in ClinVar as [Benign]. Clinvar id is 2652866.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00787 (1199/152340) while in subpopulation NFE AF= 0.0143 (970/68022). AF 95% confidence interval is 0.0135. There are 11 homozygotes in gnomad4. There are 523 alleles in male gnomad4 subpopulation. Median coverage is 35. This position pass quality control queck.
• BS2: High AC in GnomAd at 1200 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX1	NM_005992.1	c.-86-48C>G		intron_variant
TBX1	NM_080646.2	c.-86-48C>G		intron_variant
TBX1	NM_080647.1	c.-86-48C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX1	ENST00000329705.11	c.-86-48C>G		intron_variant		1		A2
TBX1	ENST00000332710.8	c.-86-48C>G		intron_variant		1		P2
TBX1	ENST00000359500.7	c.-86-48C>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.00788 AC: 1200 AN: 152222 Hom.: 11 Cov.: 35

Gnomad AFR AF: 0.00222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00517

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.00669

GnomAD4 exome AF: 0.0141 AC: 19215 AN: 1362192 Hom.: 171 Cov.: 29 AF XY: 0.0136 AC XY: 9105 AN XY: 670452

Gnomad4 AFR exome AF: 0.00204

Gnomad4 AMR exome AF: 0.00447

Gnomad4 ASJ exome AF: 0.00231

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000805

Gnomad4 FIN exome AF: 0.00380

Gnomad4 NFE exome AF: 0.0170

Gnomad4 OTH exome AF: 0.0108

GnomAD4 genome AF: 0.00787 AC: 1199 AN: 152340 Hom.: 11 Cov.: 35 AF XY: 0.00702 AC XY: 523 AN XY: 74496

Gnomad4 AFR AF: 0.00221

Gnomad4 AMR AF: 0.00510

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00348

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.00662

Alfa AF: 0.00937 Hom.: 3

Bravo AF: 0.00794

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

TBX1: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
Cadd	Benign	22
Dann	Benign	0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs72646948; hg19: chr22-19747033;