chr12-114408030-C-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2

The NM_000192.3(TBX5):​c.-255G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00187 in 985,440 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00099 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0020 ( 1 hom. )

Consequence

TBX5
NM_000192.3 5_prime_UTR

Scores

2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.97
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-AS1 (HGNC:27402): (TBX5 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000991 (151/152324) while in subpopulation NFE AF= 0.0015 (102/68034). AF 95% confidence interval is 0.00126. There are 0 homozygotes in gnomad4. There are 61 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 151 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBX5NM_000192.3 linkc.-255G>T 5_prime_UTR_variant Exon 1 of 9 NP_000183.2 Q99593-1
TBX5NM_080717.4 linkc.-220G>T upstream_gene_variant NP_542448.1 Q99593-3
TBX5XM_017019912.2 linkc.-1692G>T upstream_gene_variant XP_016875401.1
TBX5-AS1NR_038440.1 linkn.-165C>A upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBX5ENST00000310346.8 linkc.-255G>T 5_prime_UTR_variant Exon 1 of 9 1 ENSP00000309913.4 Q99593-1
TBX5ENST00000349716.9 linkc.-220G>T 5_prime_UTR_variant Exon 1 of 8 1 ENSP00000337723.5 Q99593-3
TBX5-AS1ENST00000528549.3 linkn.-104C>A upstream_gene_variant 1

Frequencies

GnomAD3 genomes
AF:
0.000992
AC:
151
AN:
152206
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.000982
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000828
Gnomad FIN
AF:
0.000753
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00150
Gnomad OTH
AF:
0.000478
GnomAD4 exome
AF:
0.00202
AC:
1687
AN:
833116
Hom.:
1
Cov.:
29
AF XY:
0.00214
AC XY:
824
AN XY:
384722
show subpopulations
Gnomad4 AFR exome
AF:
0.000127
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000790
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00214
Gnomad4 OTH exome
AF:
0.00158
GnomAD4 genome
AF:
0.000991
AC:
151
AN:
152324
Hom.:
0
Cov.:
33
AF XY:
0.000819
AC XY:
61
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.000313
Gnomad4 AMR
AF:
0.000981
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.000753
Gnomad4 NFE
AF:
0.00150
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000556
Hom.:
0
Bravo
AF:
0.00100
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Holt-Oram syndrome Uncertain:1
Jan 13, 2018
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
CADD
Benign
19
DANN
Benign
0.94

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

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

Other links and lift over

dbSNP: rs186472610; hg19: chr12-114845835; API