Genetic Variant NM_018204.5:c.70+26_70+49dupTGGCGGTGGCGGTGGCGGTGGCGG (chr13-52455635-C-CGCGGTGGCGGTGGCGGTGGCGGTG) – 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+26_70+49dupTGGCGGTGGCGGTGGCGGTGGCGG variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)

Exomes 𝑓: 7.1e-7 ( 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+26_70+49dupTGGCGGTGGCGGTGGCGGTGGCGG	intron_variant	Intron 1 of 8	ENST00000258607.10	NP_060674.3	Q8WWK9-5
CKAP2	NM_001098525.3 link	c.70+26_70+49dupTGGCGGTGGCGGTGGCGGTGGCGG	intron_variant	Intron 1 of 8		NP_001091995.1	Q8WWK9-1
CKAP2	NM_001286687.2 link	c.70+26_70+49dupTGGCGGTGGCGGTGGCGGTGGCGG	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+10insGCGGTGGCGGTGGCGGTGGCGGTG		intron_variant	Intron 1 of 8	1	NM_018204.5	ENSP00000258607.5		Q8WWK9-5

Frequencies

GnomAD3 genomes

AF:

0.00000659

AC:

AN:

151712

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

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:

7.09e-7

AC:

AN:

1411334

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

701974

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.16e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00000659

AC:

AN:

151712

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74080

show subpopulations

Gnomad4 AFR

AF:

0.0000242

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

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.

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