rs539663160
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_005994.4(TBX2):c.192_203delGGCGGCGGCGGC(p.Ala65_Ala68del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,033,728 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 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000011 ( 0 hom. )
Consequence
TBX2
NM_005994.4 disruptive_inframe_deletion
NM_005994.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.91
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_005994.4
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX2 | NM_005994.4 | c.192_203delGGCGGCGGCGGC | p.Ala65_Ala68del | disruptive_inframe_deletion | Exon 1 of 7 | ENST00000240328.4 | NP_005985.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000681 AC: 1AN: 146904Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000113 AC: 1AN: 886824Hom.: 0 AF XY: 0.00000241 AC XY: 1AN XY: 415134
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GnomAD4 genome AF: 0.00000681 AC: 1AN: 146904Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 71442
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at