rs179050

Variant names:

• chr16-19536830-T-C
• rs179050
• NM_001323572.2:c.1161T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001323572.2(CCP110):​c.1161T>C​(p.His387His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 1,614,030 control chromosomes in the GnomAD database, including 7,342 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.10 (876 hom., cov: 33)
  • Exomes 𝑓: 0.089 (6466 hom.)
• Consequence: CCP110 NM_001323572.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 9 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCP110	NM_001323572.2	MANE Select	c.1161T>C	p.His387His	synonymous	Exon 4 of 14	NP_001310501.1
	CCP110	NM_001199022.3		c.1161T>C	p.His387His	synonymous	Exon 4 of 15	NP_001185951.2
	CCP110	NM_001323569.2		c.1161T>C	p.His387His	synonymous	Exon 5 of 16	NP_001310498.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCP110	ENST00000694978.1	MANE Select	c.1161T>C	p.His387His	synonymous	Exon 4 of 14	ENSP00000511625.1
	CCP110	ENST00000381396.9	TSL:1	c.1161T>C	p.His387His	synonymous	Exon 4 of 15	ENSP00000370803.5
	CCP110	ENST00000396208.4	TSL:1	c.1161T>C	p.His387His	synonymous	Exon 3 of 13	ENSP00000379511.2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15472 AN: 152108 Hom.: 874 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.108

GnomAD2 exomes AF: 0.0759 AC: 18980 AN: 250114 AF XY: 0.0739

Gnomad AFR exome AF: 0.159

Gnomad AMR exome AF: 0.0552

Gnomad ASJ exome AF: 0.0851

Gnomad EAS exome AF: 0.000870

Gnomad FIN exome AF: 0.0707

Gnomad NFE exome AF: 0.0933

Gnomad OTH exome AF: 0.0838

GnomAD4 exome AF: 0.0891 AC: 130299 AN: 1461804 Hom.: 6466 Cov.: 38 AF XY: 0.0870 AC XY: 63276 AN XY: 727188

African (AFR) AF: 0.158 AC: 5287 AN: 33478

American (AMR) AF: 0.0572 AC: 2556 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 2150 AN: 26134

East Asian (EAS) AF: 0.000781 AC: 31 AN: 39698

South Asian (SAS) AF: 0.0372 AC: 3213 AN: 86258

European-Finnish (FIN) AF: 0.0690 AC: 3686 AN: 53390

Middle Eastern (MID) AF: 0.105 AC: 606 AN: 5768

European-Non Finnish (NFE) AF: 0.0964 AC: 107210 AN: 1111968

Other (OTH) AF: 0.0921 AC: 5560 AN: 60392

GnomAD4 genome AF: 0.102 AC: 15486 AN: 152226 Hom.: 876 Cov.: 33 AF XY: 0.0973 AC XY: 7242 AN XY: 74422

African (AFR) AF: 0.156 AC: 6460 AN: 41538

American (AMR) AF: 0.0742 AC: 1134 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4820

European-Finnish (FIN) AF: 0.0637 AC: 675 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0945 AC: 6428 AN: 68022

Other (OTH) AF: 0.108 AC: 228 AN: 2110

Alfa AF: 0.0981 Hom.: 1044

Bravo AF: 0.105

Asia WGS AF: 0.0330 AC: 113 AN: 3478

EpiCase AF: 0.0968

EpiControl AF: 0.0923

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		0.067
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs179050; hg19: chr16-19548152; COSMIC: COSV66818183; COSMIC: COSV66818183;