rs7191012

chr16-19536968-G-Achr16-19536968-G-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_001323572.2(CCP110):c.1299G>A(p.Ala433=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,614,030 control chromosomes in the GnomAD database, including 18,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (1844 hom., cov: 33)
  • Exomes 𝑓: 0.15 (17002 hom.)
• Consequence: CCP110 NM_001323572.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0260

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 -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 16-19536968-G-A is Benign according to our data. Variant chr16-19536968-G-A is described in ClinVar as [Benign]. Clinvar id is 402514.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.026 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCP110	NM_001323572.2	c.1299G>A	p.Ala433=	synonymous_variant	4/14	ENST00000694978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCP110	ENST00000694978.1	c.1299G>A	p.Ala433=	synonymous_variant	4/14		NM_001323572.2	P4

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23251 AN: 152060 Hom.: 1844 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.171

GnomAD3 exomes AF: 0.148 AC: 37289 AN: 251214 Hom.: 2941 AF XY: 0.144 AC XY: 19580 AN XY: 135806

Gnomad AFR exome AF: 0.156

Gnomad AMR exome AF: 0.192

Gnomad ASJ exome AF: 0.206

Gnomad EAS exome AF: 0.155

Gnomad SAS exome AF: 0.0861

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.151

Gnomad OTH exome AF: 0.142

GnomAD4 exome AF: 0.150 AC: 218876 AN: 1461852 Hom.: 17002 Cov.: 36 AF XY: 0.148 AC XY: 107606 AN XY: 727222

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.201

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.0854

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.153 AC: 23257 AN: 152178 Hom.: 1844 Cov.: 33 AF XY: 0.152 AC XY: 11338 AN XY: 74388

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.168

Alfa AF: 0.154 Hom.: 2380

Bravo AF: 0.162

Asia WGS AF: 0.126 AC: 440 AN: 3478

EpiCase AF: 0.153

EpiControl AF: 0.157

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.6
Dann	Benign	0.37

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: rs7191012; hg19: chr16-19548290; COSMIC: COSV66817375; COSMIC: COSV66817375;