GeneBe

rs883079

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000192.3(TBX5):​c.*97G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TBX5
NM_000192.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.967

Publications

0 publications found
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 Gene-Disease associations (from GenCC):
  • Holt-Oram syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet, G2P, Ambry Genetics
  • heart conduction disease
    Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.026).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000192.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TBX5
NM_181486.4
MANE Select
c.*97G>T
3_prime_UTR
Exon 9 of 9NP_852259.1
TBX5
NM_000192.3
c.*97G>T
3_prime_UTR
Exon 9 of 9NP_000183.2
TBX5
NM_080717.4
c.*97G>T
3_prime_UTR
Exon 8 of 8NP_542448.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TBX5
ENST00000405440.7
TSL:1 MANE Select
c.*97G>T
3_prime_UTR
Exon 9 of 9ENSP00000384152.3
TBX5
ENST00000310346.8
TSL:1
c.*97G>T
3_prime_UTR
Exon 9 of 9ENSP00000309913.4
TBX5
ENST00000349716.9
TSL:1
c.*97G>T
3_prime_UTR
Exon 8 of 8ENSP00000337723.5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1302236
Hom.:
0
Cov.:
20
AF XY:
0.00
AC XY:
0
AN XY:
649010
African (AFR)
AF:
0.00
AC:
0
AN:
30002
American (AMR)
AF:
0.00
AC:
0
AN:
36456
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24624
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36532
South Asian (SAS)
AF:
0.00
AC:
0
AN:
77520
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46578
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4998
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
990516
Other (OTH)
AF:
0.00
AC:
0
AN:
55010
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
6.2
DANN
Benign
0.83
PhyloP100
-0.97

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

Other links and lift over

dbSNP: rs883079; hg19: chr12-114793240; API