NM_005994.4:c.198_203dupGGCGGC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_005994.4(TBX2):c.198_203dupGGCGGC(p.Ala67_Ala68dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,033,830 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
TBX2
NM_005994.4 disruptive_inframe_insertion
NM_005994.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.53
Genes affected
TBX2 (HGNC:11597): (T-box transcription factor 2) 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 product is the human homolog of mouse Tbx2, and shares strong sequence similarity with Drosophila omb protein. Expression studies indicate that this gene may have a potential role in tumorigenesis as an immortalizing agent. Transcript heterogeneity due to alternative polyadenylation has been noted for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_005994.4
BS2
High AC in GnomAd4 at 34 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX2 | NM_005994.4 | c.198_203dupGGCGGC | p.Ala67_Ala68dup | disruptive_inframe_insertion | Exon 1 of 7 | ENST00000240328.4 | NP_005985.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000231 AC: 34AN: 146902Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000149 AC: 132AN: 886824Hom.: 0 Cov.: 30 AF XY: 0.000161 AC XY: 67AN XY: 415134
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GnomAD4 genome AF: 0.000231 AC: 34AN: 147006Hom.: 0 Cov.: 32 AF XY: 0.000196 AC XY: 14AN XY: 71554
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at