Genetic Variant NM_018204.5:c.70+44_70+49dupTGGCGG (chr13-52455635-C-CGCGGTG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_018204.5(CKAP2):c.70+44_70+49dupTGGCGG variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.016 ( 45 hom., cov: 0)

Exomes 𝑓: 0.0045 ( 38 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0158 (2405/151796) while in subpopulation AFR AF = 0.039 (1614/41426). AF 95% confidence interval is 0.0374. There are 45 homozygotes in GnomAd4. There are 1135 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 45 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+44_70+49dupTGGCGG	intron	N/A	NP_060674.3
CKAP2	NM_001098525.3		c.70+44_70+49dupTGGCGG	intron	N/A	NP_001091995.1	Q8WWK9-1
CKAP2	NM_001286687.2		c.70+44_70+49dupTGGCGG	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+9_70+10insGCGGTG	intron	N/A	ENSP00000258607.5	Q8WWK9-5
CKAP2	ENST00000378037.9	TSL:1	c.70+9_70+10insGCGGTG	intron	N/A	ENSP00000367276.4	Q8WWK9-1
CKAP2	ENST00000378034.7	TSL:1	c.70+9_70+10insGCGGTG	intron	N/A	ENSP00000367273.2	Q8WWK9-4

Frequencies

GnomAD3 genomes

AF:

0.0158

AC:

2396

AN:

151688

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0389

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00840

Gnomad ASJ

AF:

0.000578

Gnomad EAS

AF:

0.0326

Gnomad SAS

AF:

0.00851

Gnomad FIN

AF:

0.00503

Gnomad MID

AF:

0.00962

Gnomad NFE

AF:

0.00530

Gnomad OTH

AF:

0.0168

GnomAD2 exomes

AF:

0.00463

AC:

862

AN:

186206

AF XY:

0.00421

show subpopulations

Gnomad AFR exome

AF:

0.0155

Gnomad AMR exome

AF:

0.00285

Gnomad ASJ exome

AF:

0.000610

Gnomad EAS exome

AF:

0.0190

Gnomad FIN exome

AF:

0.00527

Gnomad NFE exome

AF:

0.00284

Gnomad OTH exome

AF:

0.00214

GnomAD4 exome

AF:

0.00445

AC:

6278

AN:

1410378

Hom.:

Cov.:

AF XY:

0.00440

AC XY:

3089

AN XY:

701464

show subpopulations

African (AFR)

AF:

0.0222

AC:

639

AN:

28748

American (AMR)

AF:

0.00343

AC:

128

AN:

37342

Ashkenazi Jewish (ASJ)

AF:

0.000529

AC:

AN:

24568

East Asian (EAS)

AF:

0.0192

AC:

656

AN:

34140

South Asian (SAS)

AF:

0.00414

AC:

336

AN:

81238

European-Finnish (FIN)

AF:

0.00478

AC:

243

AN:

50840

Middle Eastern (MID)

AF:

0.00217

AC:

AN:

5060

European-Non Finnish (NFE)

AF:

0.00360

AC:

3923

AN:

1090696

Other (OTH)

AF:

0.00570

AC:

329

AN:

57746

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.406

Heterozygous variant carriers

226

451

677

902

1128

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

180

360

540

720

900

<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:

0.0158

AC:

2405

AN:

151796

Hom.:

Cov.:

AF XY:

0.0153

AC XY:

1135

AN XY:

74184

show subpopulations

African (AFR)

AF:

0.0390

AC:

1614

AN:

41426

American (AMR)

AF:

0.00839

AC:

128

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.000578

AC:

AN:

3462

East Asian (EAS)

AF:

0.0329

AC:

169

AN:

5142

South Asian (SAS)

AF:

0.00852

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00503

AC:

AN:

10528

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00530

AC:

360

AN:

67870

Other (OTH)

AF:

0.0166

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

105

210

316

421

526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

150

<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:

0.00186

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

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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