ENST00000526441.1:c.998C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000526441.1(TBX5):c.998C>T(p.Pro333Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00881 in 1,610,238 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0066 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0090 ( 69 hom. )

Consequence

TBX5
ENST00000526441.1 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 0.0580

Variant links:

Genes affected

TBX5 (HGNC:11604): (T-box transcription factor 5) 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 is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

TBX5 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=0.0057828724).

BP6

Variant 12-114366149-G-A is Benign according to our data. Variant chr12-114366149-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 255494.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-114366149-G-A is described in Lovd as [Benign]. Variant chr12-114366149-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00664 (1011/152264) while in subpopulation NFE AF= 0.0107 (726/68018). AF 95% confidence interval is 0.01. There are 5 homozygotes in gnomad4. There are 476 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1011 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TBX5	NM_181486.4 link	c.982+16C>T	intron_variant	Intron 8 of 8	ENST00000405440.7	NP_852259.1	Q99593-1
TBX5	NM_000192.3 link	c.982+16C>T	intron_variant	Intron 8 of 8		NP_000183.2	Q99593-1
TBX5	NM_080717.4 link	c.832+16C>T	intron_variant	Intron 7 of 7		NP_542448.1	Q99593-3
TBX5	XM_017019912.2 link	c.1030+16C>T	intron_variant	Intron 8 of 8		XP_016875401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBX5	ENST00000526441.1 link	c.998C>T	p.Pro333Leu	missense_variant	Exon 7 of 7	1		ENSP00000433292.1	Q99593-2
TBX5	ENST00000405440.7 link	c.982+16C>T		intron_variant	Intron 8 of 8	1	NM_181486.4	ENSP00000384152.3	Q99593-1
TBX5	ENST00000310346.8 link	c.982+16C>T		intron_variant	Intron 8 of 8	1		ENSP00000309913.4	Q99593-1
TBX5	ENST00000349716.9 link	c.832+16C>T		intron_variant	Intron 7 of 7	1		ENSP00000337723.5	Q99593-3

Frequencies

GnomAD3 genomes

AF:

0.00664

AC:

1011

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00838

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00396

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00545

AC:

1370

AN:

251348

Hom.:

AF XY:

0.00561

AC XY:

762

AN XY:

135846

show subpopulations

Gnomad AFR exome

AF:

0.00191

Gnomad AMR exome

AF:

0.00425

Gnomad ASJ exome

AF:

0.00268

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000751

Gnomad FIN exome

AF:

0.00374

Gnomad NFE exome

AF:

0.00904

Gnomad OTH exome

AF:

0.00538

GnomAD4 exome

AF:

0.00903

AC:

13168

AN:

1457974

Hom.:

Cov.:

AF XY:

0.00865

AC XY:

6275

AN XY:

725484

show subpopulations

Gnomad4 AFR exome

AF:

0.00132

Gnomad4 AMR exome

AF:

0.00472

Gnomad4 ASJ exome

AF:

0.00272

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000789

Gnomad4 FIN exome

AF:

0.00361

Gnomad4 NFE exome

AF:

0.0109

Gnomad4 OTH exome

AF:

0.00753

GnomAD4 genome

AF:

0.00664

AC:

1011

AN:

152264

Hom.:

Cov.:

AF XY:

0.00639

AC XY:

476

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00217

Gnomad4 AMR

AF:

0.00837

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00396

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00866

Hom.:

Bravo

AF:

0.00675

TwinsUK

AF:

0.0113

AC:

ALSPAC

AF:

0.0106

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.00965

AC:

ExAC

AF:

0.00533

AC:

647

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00883

EpiControl

AF:

0.00966

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:5

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

TBX5: BP4, BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 28, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:3

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 14, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aortic valve disease 2

Benign:1

Feb 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.37

CADD

Benign

1.3

DANN

Benign

0.57

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.67

FATHMM_MKL

Benign

0.23

LIST_S2

Benign

0.29

M_CAP

Benign

0.011

MetaRNN

Benign

0.0058

MetaSVM

Benign

-0.49

PROVEAN

Benign

-1.5

REVEL

Benign

0.21

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

1.0

Vest4

0.23

MVP

0.61

ClinPred

0.015

GERP RS

2.6

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