Genetic Variant CKAP2:c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG (chr13-52455635-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_018204.5(CKAP2):c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG variant causes a intron change. The variant allele was found at a frequency of 0.000947 in 1,563,148 control chromosomes in the GnomAD database, including 5 homozygotes. 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 0.00084 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00096 ( 4 hom. )

Consequence

CKAP2
NM_018204.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.63

Publications

2 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 4 AR gene

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CKAP2	NM_018204.5	MANE Select	c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG	intron	N/A	NP_060674.3
CKAP2	NM_001098525.3		c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG	intron	N/A	NP_001091995.1	Q8WWK9-1
CKAP2	NM_001286687.2		c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG	intron	N/A	NP_001273616.1	Q8WWK9-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CKAP2	ENST00000258607.10	TSL:1 MANE Select	c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG	intron	N/A	ENSP00000258607.5	Q8WWK9-5
CKAP2	ENST00000378037.9	TSL:1	c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG	intron	N/A	ENSP00000367276.4	Q8WWK9-1
CKAP2	ENST00000378034.7	TSL:1	c.70+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG	intron	N/A	ENSP00000367273.2	Q8WWK9-4

Frequencies

GnomAD3 genomes

AF:

0.000837

AC:

127

AN:

151712

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000919

Gnomad ASJ

AF:

0.000578

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000285

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00143

Gnomad OTH

AF:

0.000479

GnomAD2 exomes

AF:

0.000897

AC:

167

AN:

186206

AF XY:

0.000873

show subpopulations

Gnomad AFR exome

AF:

0.000122

Gnomad AMR exome

AF:

0.000562

Gnomad ASJ exome

AF:

0.000610

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000256

Gnomad NFE exome

AF:

0.00165

Gnomad OTH exome

AF:

0.000238

GnomAD4 exome

AF:

0.000959

AC:

1353

AN:

1411328

Hom.:

AF XY:

0.000973

AC XY:

683

AN XY:

701972

show subpopulations

African (AFR)

AF:

0.000174

AC:

AN:

28798

American (AMR)

AF:

0.000776

AC:

AN:

37358

Ashkenazi Jewish (ASJ)

AF:

0.000448

AC:

AN:

24568

East Asian (EAS)

AF:

0.00

AC:

AN:

34296

South Asian (SAS)

AF:

0.0000368

AC:

AN:

81422

European-Finnish (FIN)

AF:

0.000196

AC:

AN:

50898

Middle Eastern (MID)

AF:

0.000593

AC:

AN:

5060

European-Non Finnish (NFE)

AF:

0.00114

AC:

1240

AN:

1091136

Other (OTH)

AF:

0.000900

AC:

AN:

57792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

115

173

230

288

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000837

AC:

127

AN:

151820

Hom.:

Cov.:

AF XY:

0.000782

AC XY:

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.000241

AC:

AN:

41438

American (AMR)

AF:

0.000918

AC:

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.000578

AC:

AN:

3462

East Asian (EAS)

AF:

0.00

AC:

AN:

5144

South Asian (SAS)

AF:

0.00

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.000285

AC:

AN:

10530

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00143

AC:

AN:

67876

Other (OTH)

AF:

0.000475

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000857

Hom.:

1803

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.6

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over