22-19766568-A-C

Position:

chr22-19766568-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001379200.1(TBX1):c.1216A>C(p.Asn406His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,441,986 control chromosomes in the GnomAD database, including 37,415 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3490 hom., cov: 32)

Exomes 𝑓: 0.22 ( 33925 hom. )

Consequence

TBX1
NM_001379200.1 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 2.14

Variant links:

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]

TBX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002857238).

BP6

Variant 22-19766568-A-C is Benign according to our data. Variant chr22-19766568-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 263351.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-19766568-A-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX1	NM_001379200.1 linkuse as main transcript	c.1216A>C	p.Asn406His	missense_variant	7/7	ENST00000649276.2	NP_001366129.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TBX1	ENST00000649276.2 linkuse as main transcript	c.1216A>C	p.Asn406His	missense_variant	7/7		NM_001379200.1	ENSP00000497003.1	A0A3B3IS18
TBX1	ENST00000332710.8 linkuse as main transcript	c.1189A>C	p.Asn397His	missense_variant	9/9	1		ENSP00000331791.4	O43435-3
TBX1	ENST00000329705.11 linkuse as main transcript	c.1009+566A>C		intron_variant		1		ENSP00000331176.7	O43435-1
TBX1	ENST00000359500.7 linkuse as main transcript	c.1009+566A>C		intron_variant		1		ENSP00000352483.3	O43435-2

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

27927

AN:

150614

Hom.:

3492

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0457

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.485

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.251

AC:

20007

AN:

79850

Hom.:

2801

AF XY:

0.244

AC XY:

11261

AN XY:

46122

show subpopulations

Gnomad AFR exome

AF:

0.0373

Gnomad AMR exome

AF:

0.326

Gnomad ASJ exome

AF:

0.301

Gnomad EAS exome

AF:

0.483

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.152

Gnomad NFE exome

AF:

0.220

Gnomad OTH exome

AF:

0.226

GnomAD4 exome

AF:

0.221

AC:

285760

AN:

1291264

Hom.:

33925

Cov.:

AF XY:

0.222

AC XY:

141502

AN XY:

636556

show subpopulations

Gnomad4 AFR exome

AF:

0.0354

Gnomad4 AMR exome

AF:

0.311

Gnomad4 ASJ exome

AF:

0.307

Gnomad4 EAS exome

AF:

0.471

Gnomad4 SAS exome

AF:

0.226

Gnomad4 FIN exome

AF:

0.162

Gnomad4 NFE exome

AF:

0.217

Gnomad4 OTH exome

AF:

0.220

GnomAD4 genome

AF:

0.185

AC:

27922

AN:

150722

Hom.:

3490

Cov.:

AF XY:

0.188

AC XY:

13808

AN XY:

73626

show subpopulations

Gnomad4 AFR

AF:

0.0456

Gnomad4 AMR

AF:

0.270

Gnomad4 ASJ

AF:

0.321

Gnomad4 EAS

AF:

0.484

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.204

Alfa

AF:

0.211

Hom.:

640

Bravo

AF:

0.186

TwinsUK

AF:

0.217

AC:

806

ALSPAC

AF:

0.210

AC:

810

ESP6500AA

AF:

0.0304

AC:

ESP6500EA

AF:

0.150

AC:

825

ExAC

AF:

0.143

AC:

12700

Asia WGS

AF:

0.300

AC:

1006

AN:

3342

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 16, 2016	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 04, 2023	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 07, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

DiGeorge syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Cardiovascular phenotype

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 12, 2015

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.87

Eigen

Benign

-0.92

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.25

T;T

MetaRNN

Benign

0.0029

T;T

MetaSVM

Benign

-1.0

PrimateAI

Pathogenic

0.93

PROVEAN

Benign

0.91

N;.

REVEL

Benign

0.22

Sift

Benign

1.0

T;.

Sift4G

Benign

1.0

T;.

Vest4

0.072

MPC

0.55

ClinPred

0.0012

GERP RS

2.9

gMVP

0.27

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over