rs3809627
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000553607.1(TBX6):c.-646G>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 0.415 in 152,336 control chromosomes in the GnomAD database, including 13,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.41 ( 13496 hom., cov: 33)
Exomes 𝑓: 0.35 ( 12 hom. )
Consequence
TBX6
ENST00000553607.1 5_prime_UTR
ENST00000553607.1 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.838
Genes affected
TBX6 (HGNC:11605): (T-box transcription factor 6) 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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 16-30091839-C-A is Benign according to our data. Variant chr16-30091839-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 427809.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1}.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX6 | NM_004608.4 | c.-49+34G>T | intron_variant | ENST00000395224.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX6 | ENST00000553607.1 | c.-646G>T | 5_prime_UTR_variant | 1/5 | 1 | ||||
TBX6 | ENST00000395224.7 | c.-49+34G>T | intron_variant | 1 | NM_004608.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.415 AC: 63030AN: 152034Hom.: 13469 Cov.: 33
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GnomAD4 exome AF: 0.348 AC: 64AN: 184Hom.: 12 Cov.: 0 AF XY: 0.358 AC XY: 48AN XY: 134
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GnomAD4 genome ? AF: 0.415 AC: 63089AN: 152152Hom.: 13496 Cov.: 33 AF XY: 0.421 AC XY: 31330AN XY: 74374
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Spondylocostal dysostosis 5 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Feb 18, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at