chr13-52455635-C-CGCGGTGGCGGTGGCGGTG

Variant names:

• chr13-52455635-C-CGCGGTGGCGGTGGCGGTG
• rs72440971
• NM_018204.5:c.70+32_70+49dupTGGCGGTGGCGGTGGCGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018204.5(CKAP2):​c.70+32_70+49dupTGGCGGTGGCGGTGGCGG variant causes a intron change. It is difficult to determine the true allele frequency of this variant because it is of type INS_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 0.00029 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000075 (1 hom.)
• Consequence: CKAP2 NM_018204.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.63
• Publications: 2 publications found

Genes affected

CKAP2 (HGNC:1990): (cytoskeleton associated protein 2) This gene encodes a cytoskeleton-associated protein that stabalizes microtubules and plays a role in the regulation of cell division. The encoded protein is itself regulated through phosphorylation at multiple serine and threonine residues. There is a pseudogene of this gene on chromosome 14. Alternative splicing results in multiple transcript variations. [provided by RefSeq, Nov 2013]

CKAP2-DT (HGNC:56053): (CKAP2 divergent transcript)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018204.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CKAP2	NM_018204.5	MANE Select	c.70+32_70+49dupTGGCGGTGGCGGTGGCGG		intron	N/A	NP_060674.3
	CKAP2	NM_001098525.3		c.70+32_70+49dupTGGCGGTGGCGGTGGCGG		intron	N/A	NP_001091995.1	Q8WWK9-1
	CKAP2	NM_001286687.2		c.70+32_70+49dupTGGCGGTGGCGGTGGCGG		intron	N/A	NP_001273616.1	Q8WWK9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CKAP2	ENST00000258607.10	TSL:1 MANE Select	c.70+9_70+10insGCGGTGGCGGTGGCGGTG		intron	N/A	ENSP00000258607.5	Q8WWK9-5
	CKAP2	ENST00000378037.9	TSL:1	c.70+9_70+10insGCGGTGGCGGTGGCGGTG		intron	N/A	ENSP00000367276.4	Q8WWK9-1
	CKAP2	ENST00000378034.7	TSL:1	c.70+9_70+10insGCGGTGGCGGTGGCGGTG		intron	N/A	ENSP00000367273.2	Q8WWK9-4

Frequencies

GnomAD3 genomes AF: 0.000290 AC: 44 AN: 151712 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000726

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00294

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.000479

GnomAD4 exome AF: 0.0000751 AC: 106 AN: 1411268 Hom.: 1 Cov.: 0 AF XY: 0.0000712 AC XY: 50 AN XY: 701940

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 28798

American (AMR) AF: 0.0000268 AC: 1 AN: 37356

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24570

East Asian (EAS) AF: 0.00 AC: 0 AN: 34296

South Asian (SAS) AF: 0.0000368 AC: 3 AN: 81420

European-Finnish (FIN) AF: 0.00126 AC: 64 AN: 50858

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5062

European-Non Finnish (NFE) AF: 0.0000321 AC: 35 AN: 1091122

Other (OTH) AF: 0.0000519 AC: 3 AN: 57786

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.000290 AC: 44 AN: 151712 Hom.: 0 Cov.: 0 AF XY: 0.000405 AC XY: 30 AN XY: 74080

African (AFR) AF: 0.0000726 AC: 3 AN: 41318

American (AMR) AF: 0.000131 AC: 2 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00294 AC: 31 AN: 10530

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

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 67886

Other (OTH) AF: 0.000479 AC: 1 AN: 2086

Alfa AF: 0.00 Hom.: 1803

Bravo AF: 0.0000831

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs72440971; hg19: chr13-53029770;