rs179050

Positions:

• chr16-19536830-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001323572.2(CCP110):​c.1161T>C​(p.His387=) 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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCP110	NM_001323572.2	c.1161T>C	p.His387=	synonymous_variant	4/14	ENST00000694978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCP110	ENST00000694978.1	c.1161T>C	p.His387=	synonymous_variant	4/14		NM_001323572.2	P4

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

GnomAD3 exomes AF: 0.0759 AC: 18980 AN: 250114 Hom.: 937 AF XY: 0.0739 AC XY: 10016 AN XY: 135528

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 SAS exome AF: 0.0361

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

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.0572

Gnomad4 ASJ exome AF: 0.0823

Gnomad4 EAS exome AF: 0.000781

Gnomad4 SAS exome AF: 0.0372

Gnomad4 FIN exome AF: 0.0690

Gnomad4 NFE exome AF: 0.0964

Gnomad4 OTH exome AF: 0.0921

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0637

Gnomad4 NFE AF: 0.0945

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0966 Hom.: 811

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.4
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

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