13-52455635-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG

Variant names:

• chr13-52455635-C-CGCGGTG
• rs72440971
• NM_018204.5:c.70+44_70+49dupTGGCGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

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
• 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: 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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.: 44 Cov.: 0

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

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.: 38 Cov.: 0 AF XY: 0.00440 AC XY: 3089 AN XY: 701464

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: 13 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: 11 AN: 5060

European-Non Finnish (NFE) AF: 0.00360 AC: 3923 AN: 1090696

Other (OTH) AF: 0.00570 AC: 329 AN: 57746

GnomAD4 genome AF: 0.0158 AC: 2405 AN: 151796 Hom.: 45 Cov.: 0 AF XY: 0.0153 AC XY: 1135 AN XY: 74184

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: 2 AN: 3462

East Asian (EAS) AF: 0.0329 AC: 169 AN: 5142

South Asian (SAS) AF: 0.00852 AC: 41 AN: 4812

European-Finnish (FIN) AF: 0.00503 AC: 53 AN: 10528

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 290

European-Non Finnish (NFE) AF: 0.00530 AC: 360 AN: 67870

Other (OTH) AF: 0.0166 AC: 35 AN: 2106

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

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;