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. Variant got -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

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

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 45 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CKAP2	NM_018204.5	c.70+44_70+49dupTGGCGG		intron_variant	Intron 1 of 8	ENST00000258607.10	NP_060674.3
CKAP2	NM_001098525.3	c.70+44_70+49dupTGGCGG		intron_variant	Intron 1 of 8		NP_001091995.1
CKAP2	NM_001286687.2	c.70+44_70+49dupTGGCGG		intron_variant	Intron 1 of 5		NP_001273616.1

Ensembl

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

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

GnomAD3 exomes AF: 0.00463 AC: 862 AN: 186206 Hom.: 5 AF XY: 0.00421 AC XY: 443 AN XY: 105348

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 SAS exome AF: 0.00385

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

Gnomad4 AFR exome AF: 0.0222

Gnomad4 AMR exome AF: 0.00343

Gnomad4 ASJ exome AF: 0.000529

Gnomad4 EAS exome AF: 0.0192

Gnomad4 SAS exome AF: 0.00414

Gnomad4 FIN exome AF: 0.00478

Gnomad4 NFE exome AF: 0.00360

Gnomad4 OTH exome AF: 0.00570

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

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.00839

Gnomad4 ASJ AF: 0.000578

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.00852

Gnomad4 FIN AF: 0.00503

Gnomad4 NFE AF: 0.00530

Gnomad4 OTH AF: 0.0166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72440971; hg19: chr13-53029770;