chr22-19759963-G-T

Position:

• chr22-19759963-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_080647.1(TBX1):​c.34+286G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 152,346 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.014 (31 hom., cov: 33)
• Consequence: TBX1 NM_080647.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.69

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 22-19759963-G-T is Benign according to our data. Variant chr22-19759963-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1209124.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0141 (2152/152346) while in subpopulation SAS AF= 0.039 (188/4826). AF 95% confidence interval is 0.0344. There are 31 homozygotes in gnomad4. There are 1103 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 2152 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX1	NM_080647.1	c.34+286G>T		intron_variant			NP_542378.1
TBX1	NM_080646.2	c.34+286G>T		intron_variant			NP_542377.1
TBX1	NM_005992.1	c.34+286G>T		intron_variant			NP_005983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBX1	ENST00000332710.8	c.34+286G>T		intron_variant		1		ENSP00000331791.4
TBX1	ENST00000329705.11	c.34+286G>T		intron_variant		1		ENSP00000331176.7
TBX1	ENST00000359500.7	c.34+286G>T		intron_variant		1		ENSP00000352483.3

Frequencies

GnomAD3 genomes AF: 0.0141 AC: 2144 AN: 152228 Hom.: 28 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00739

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0141 AC: 2152 AN: 152346 Hom.: 31 Cov.: 33 AF XY: 0.0148 AC XY: 1103 AN XY: 74502

Gnomad4 AFR AF: 0.0122

Gnomad4 AMR AF: 0.00738

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0113

Alfa AF: 0.00341 Hom.: 1

Bravo AF: 0.0126

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.55
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs41298790; hg19: chr22-19747486;