16-19536360-CTG-TTA

Variant names:

• chr16-19536360-CTG-TTA
• NM_001323572.2:c.691_693delCTGinsTTA
• CCP110 p.232

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001323572.2(CCP110):​c.691_693delCTGinsTTA​(p.232) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, 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: not found (cov: 32)
• Consequence: CCP110 NM_001323572.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.50
• Publications: 0 publications found

Genes affected

CCP110 (HGNC:24342): (centriolar coiled-coil protein 110) Involved in centriole replication; negative regulation of cilium assembly; and regulation of cytokinesis. Located in centriole and centrosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

CCP110 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323572.2. 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
	CCP110	NM_001323572.2	MANE Select	c.691_693delCTGinsTTA	p.232	synonymous	N/A	NP_001310501.1	O43303-2
	CCP110	NM_001199022.3		c.691_693delCTGinsTTA	p.232	synonymous	N/A	NP_001185951.2	O43303-1
	CCP110	NM_001323569.2		c.691_693delCTGinsTTA	p.232	synonymous	N/A	NP_001310498.1	O43303-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCP110	ENST00000694978.1	MANE Select	c.691_693delCTGinsTTA	p.232	synonymous	N/A	ENSP00000511625.1	O43303-2
	CCP110	ENST00000381396.9	TSL:1	c.691_693delCTGinsTTA	p.232	synonymous	N/A	ENSP00000370803.5	O43303-1
	CCP110	ENST00000396208.4	TSL:1	c.691_693delCTGinsTTA	p.232	synonymous	N/A	ENSP00000379511.2	O43303-2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-19547682;