chr6-166160857-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001366285.2(TBXT):c.1017C>A(p.Ala339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
TBXT
NM_001366285.2 synonymous
NM_001366285.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.415
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 6-166160857-G-T is Benign according to our data. Variant chr6-166160857-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3057549.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.415 with no splicing effect.
BS2
High AC in GnomAd4 at 26 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXT | NM_001366285.2 | c.1017C>A | p.Ala339= | synonymous_variant | 7/8 | ENST00000366876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXT | ENST00000366876.7 | c.1017C>A | p.Ala339= | synonymous_variant | 7/8 | 1 | NM_001366285.2 | P4 | |
TBXT | ENST00000366871.7 | c.840C>A | p.Ala280= | synonymous_variant | 7/8 | 1 | |||
TBXT | ENST00000296946.6 | c.1014C>A | p.Ala338= | synonymous_variant | 8/9 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152208Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000954 AC: 24AN: 251454Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135900
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GnomAD4 exome AF: 0.000101 AC: 148AN: 1461832Hom.: 0 Cov.: 33 AF XY: 0.000109 AC XY: 79AN XY: 727214
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GnomAD4 genome AF: 0.000171 AC: 26AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74364
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TBXT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 05, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at