6-166160758-G-A
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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
NM_001366285.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.346
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 |
---|---|---|---|---|---|---|---|
TBXT | NM_001366285.2 | c.1037+79C>T | intron_variant | ENST00000366876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXT | ENST00000366876.7 | c.1037+79C>T | intron_variant | 1 | NM_001366285.2 | P4 | |||
TBXT | ENST00000366871.7 | c.860+79C>T | intron_variant | 1 | |||||
TBXT | ENST00000296946.6 | c.1034+79C>T | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.765 AC: 116260AN: 151944Hom.: 44810 Cov.: 31
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GnomAD4 exome AF: 0.742 AC: 1071658AN: 1444202Hom.: 398830 AF XY: 0.740 AC XY: 530950AN XY: 717190
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GnomAD4 genome AF: 0.765 AC: 116369AN: 152062Hom.: 44859 Cov.: 31 AF XY: 0.762 AC XY: 56649AN XY: 74326
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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 provided | literature only | OMIM | Nov 01, 2004 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at