rs539663160

Variant names:

• chr17-61400362-CGCGGCGGCGGCG-C
• rs539663160
• NM_005994.4:c.192_203delGGCGGCGGCGGC

Your query was ambiguous. Multiple possible variants found:

• chr17-61400362-CGCGGCGGCGGCG-C
• chr17-61400362-CGCGGCGGCGGCG-CGCG
• chr17-61400362-CGCGGCGGCGGCG-CGCGGCG
• chr17-61400362-CGCGGCGGCGGCG-CGCGGCGGCG
• chr17-61400362-CGCGGCGGCGGCG-CGCGGCGGCGGCGGCG
• chr17-61400362-CGCGGCGGCGGCG-CGCGGCGGCGGCGGCGGCG
• chr17-61400362-CGCGGCGGCGGCG-CGCGGCGGCGGCGGCGGCGGCG

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91
• Publications: 0 publications found

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]

TBX2-AS1 (HGNC:50355): (TBX2 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• 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

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX2	ENST00000240328.4	c.192_203delGGCGGCGGCGGC	p.Ala65_Ala68del	disruptive_inframe_deletion	Exon 1 of 7	1	NM_005994.4	ENSP00000240328.3

Frequencies

GnomAD3 genomes AF: 0.00000681 AC: 1 AN: 146904 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000113 AC: 1 AN: 886824 Hom.: 0 AF XY: 0.00000241 AC XY: 1 AN XY: 415134

African (AFR) AF: 0.00 AC: 0 AN: 16918

American (AMR) AF: 0.00 AC: 0 AN: 2438

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6546

East Asian (EAS) AF: 0.000141 AC: 1 AN: 7116

South Asian (SAS) AF: 0.00 AC: 0 AN: 17832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5574

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1934

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 798124

Other (OTH) AF: 0.00 AC: 0 AN: 30342

GnomAD4 genome AF: 0.00000681 AC: 1 AN: 146904 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 71442

African (AFR) AF: 0.00 AC: 0 AN: 40896

American (AMR) AF: 0.00 AC: 0 AN: 14784

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3392

East Asian (EAS) AF: 0.000196 AC: 1 AN: 5098

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8648

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66018

Other (OTH) AF: 0.00 AC: 0 AN: 2022

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9
Mutation Taster		=187/13	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs539663160; hg19: chr17-59477723;