Genetic Variant CKAP2:c.70+38_70+49dupTGGCGGTGGCGG (chr13-52455635-C-CGCGGTGGCGGTG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_018204.5(CKAP2):c.70+38_70+49dupTGGCGGTGGCGG variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00038 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00028 ( 0 hom. )

Consequence

CKAP2
NM_018204.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.63

Variant links:

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 links:

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

CKAP2-DT links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CKAP2	NM_018204.5 link	c.70+38_70+49dupTGGCGGTGGCGG	intron_variant	Intron 1 of 8	ENST00000258607.10	NP_060674.3	Q8WWK9-5
CKAP2	NM_001098525.3 link	c.70+38_70+49dupTGGCGGTGGCGG	intron_variant	Intron 1 of 8		NP_001091995.1	Q8WWK9-1
CKAP2	NM_001286687.2 link	c.70+38_70+49dupTGGCGGTGGCGG	intron_variant	Intron 1 of 5		NP_001273616.1	Q8WWK9-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CKAP2	ENST00000258607.10 link	c.70+9_70+10insGCGGTGGCGGTG		intron_variant	Intron 1 of 8	1	NM_018204.5	ENSP00000258607.5		Q8WWK9-5

Frequencies

GnomAD3 genomes

AF:

0.000376

AC:

AN:

151710

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000654

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000656

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000581

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000383

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000277

AC:

391

AN:

1411258

Hom.:

Cov.:

AF XY:

0.000275

AC XY:

193

AN XY:

701940

show subpopulations

Gnomad4 AFR exome

AF:

0.000278

Gnomad4 AMR exome

AF:

0.000294

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000117

Gnomad4 SAS exome

AF:

0.000184

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000306

Gnomad4 OTH exome

AF:

0.000311

GnomAD4 genome

AF:

0.000382

AC:

AN:

151818

Hom.:

Cov.:

AF XY:

0.000270

AC XY:

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.000676

Gnomad4 AMR

AF:

0.0000656

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000583

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000383

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

13-52455635-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over