NM_018204.5:c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG

Variant names:

• chr13-52455635-CGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG-C
• rs72440971
• NM_018204.5:c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG

Variant summary

Our verdict is Likely benign. Variant got -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. 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
• 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CKAP2	NM_018204.5	c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG		intron_variant	Intron 1 of 8	ENST00000258607.10	NP_060674.3
CKAP2	NM_001098525.3	c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG		intron_variant	Intron 1 of 8		NP_001091995.1
CKAP2	NM_001286687.2	c.70+20_70+49delTGGCGGTGGCGGTGGCGGTGGCGGTGGCGG		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+10_70+39delGCGGTGGCGGTGGCGGTGGCGGTGGCGGTG		intron_variant	Intron 1 of 8	1	NM_018204.5	ENSP00000258607.5

Frequencies

GnomAD3 genomes AF: 0.000837 AC: 127 AN: 151712 Hom.: 1 Cov.: 0

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

GnomAD3 exomes AF: 0.000897 AC: 167 AN: 186206 Hom.: 5 AF XY: 0.000873 AC XY: 92 AN XY: 105348

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 SAS exome AF: 0.0000397

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.: 4 AF XY: 0.000973 AC XY: 683 AN XY: 701972

Gnomad4 AFR exome AF: 0.000174

Gnomad4 AMR exome AF: 0.000776

Gnomad4 ASJ exome AF: 0.000448

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000368

Gnomad4 FIN exome AF: 0.000196

Gnomad4 NFE exome AF: 0.00114

Gnomad4 OTH exome AF: 0.000900

GnomAD4 genome AF: 0.000837 AC: 127 AN: 151820 Hom.: 1 Cov.: 0 AF XY: 0.000782 AC XY: 58 AN XY: 74200

Gnomad4 AFR AF: 0.000241

Gnomad4 AMR AF: 0.000918

Gnomad4 ASJ AF: 0.000578

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000285

Gnomad4 NFE AF: 0.00143

Gnomad4 OTH AF: 0.000475

Alfa AF: 0.000857 Hom.: 1803

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;