6-166160758-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001366285.2(TBXT):​c.1037+79C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 1,596,264 control chromosomes in the GnomAD database, including 443,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.77 ( 44859 hom., cov: 31)
Exomes 𝑓: 0.74 ( 398830 hom. )

Consequence

TBXT
NM_001366285.2 intron

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: 0.346
Variant links:
Genes affected
TBXT (HGNC:11515): (T-box transcription factor T) The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for mesoderm formation and differentiation. The protein is localized to notochord-derived cells. Variation in this gene was associated with susceptibility to neural tube defects and chordoma. A mutation in this gene was found in a family with sacral agenesis with vertebral anomalies. [provided by RefSeq, Sep 2018]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TBXTNM_001366285.2 linkuse as main transcriptc.1037+79C>T intron_variant ENST00000366876.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TBXTENST00000366876.7 linkuse as main transcriptc.1037+79C>T intron_variant 1 NM_001366285.2 P4
TBXTENST00000366871.7 linkuse as main transcriptc.860+79C>T intron_variant 1 O15178-2
TBXTENST00000296946.6 linkuse as main transcriptc.1034+79C>T intron_variant 5 A1O15178-1

Frequencies

GnomAD3 genomes
AF:
0.765
AC:
116260
AN:
151944
Hom.:
44810
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.849
Gnomad AMI
AF:
0.623
Gnomad AMR
AF:
0.727
Gnomad ASJ
AF:
0.732
Gnomad EAS
AF:
0.892
Gnomad SAS
AF:
0.757
Gnomad FIN
AF:
0.666
Gnomad MID
AF:
0.696
Gnomad NFE
AF:
0.733
Gnomad OTH
AF:
0.752
GnomAD4 exome
AF:
0.742
AC:
1071658
AN:
1444202
Hom.:
398830
AF XY:
0.740
AC XY:
530950
AN XY:
717190
show subpopulations
Gnomad4 AFR exome
AF:
0.855
Gnomad4 AMR exome
AF:
0.734
Gnomad4 ASJ exome
AF:
0.725
Gnomad4 EAS exome
AF:
0.875
Gnomad4 SAS exome
AF:
0.746
Gnomad4 FIN exome
AF:
0.673
Gnomad4 NFE exome
AF:
0.737
Gnomad4 OTH exome
AF:
0.759
GnomAD4 genome
AF:
0.765
AC:
116369
AN:
152062
Hom.:
44859
Cov.:
31
AF XY:
0.762
AC XY:
56649
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.849
Gnomad4 AMR
AF:
0.727
Gnomad4 ASJ
AF:
0.732
Gnomad4 EAS
AF:
0.892
Gnomad4 SAS
AF:
0.758
Gnomad4 FIN
AF:
0.666
Gnomad4 NFE
AF:
0.733
Gnomad4 OTH
AF:
0.756
Alfa
AF:
0.754
Hom.:
6341
Bravo
AF:
0.776
Asia WGS
AF:
0.840
AC:
2921
AN:
3478

ClinVar

Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Neural tube defects, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMNov 01, 2004- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.1
DANN
Benign
0.56

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.

Other links and lift over

dbSNP: rs3127334; hg19: chr6-166574246; API