16-19536035-A-G

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.366A>G(p.Thr122=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 1,613,528 control chromosomes in the GnomAD database, including 12,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (2115 hom., cov: 32)
  • Exomes 𝑓: 0.094 (10243 hom.)
• Consequence: CCP110 NM_001323572.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.267

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=-0.85).
• BP6: Variant 16-19536035-A-G is Benign according to our data. Variant chr16-19536035-A-G is described in ClinVar as [Benign]. Clinvar id is 402510.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.267 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCP110	NM_001323572.2	c.366A>G	p.Thr122=	synonymous_variant	4/14	ENST00000694978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCP110	ENST00000694978.1	c.366A>G	p.Thr122=	synonymous_variant	4/14		NM_001323572.2	P4

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21207 AN: 152028 Hom.: 2102 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.130

GnomAD3 exomes AF: 0.141 AC: 35411 AN: 251184 Hom.: 4193 AF XY: 0.132 AC XY: 17902 AN XY: 135790

Gnomad AFR exome AF: 0.221

Gnomad AMR exome AF: 0.286

Gnomad ASJ exome AF: 0.0442

Gnomad EAS exome AF: 0.418

Gnomad SAS exome AF: 0.125

Gnomad FIN exome AF: 0.0693

Gnomad NFE exome AF: 0.0690

Gnomad OTH exome AF: 0.108

GnomAD4 exome AF: 0.0942 AC: 137634 AN: 1461382 Hom.: 10243 Cov.: 32 AF XY: 0.0940 AC XY: 68331 AN XY: 727010

Gnomad4 AFR exome AF: 0.229

Gnomad4 AMR exome AF: 0.283

Gnomad4 ASJ exome AF: 0.0426

Gnomad4 EAS exome AF: 0.390

Gnomad4 SAS exome AF: 0.129

Gnomad4 FIN exome AF: 0.0690

Gnomad4 NFE exome AF: 0.0711

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.140 AC: 21251 AN: 152146 Hom.: 2115 Cov.: 32 AF XY: 0.143 AC XY: 10673 AN XY: 74388

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0895 Hom.: 1677

Bravo AF: 0.155

Asia WGS AF: 0.237 AC: 821 AN: 3478

EpiCase AF: 0.0739

EpiControl AF: 0.0741

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	-0.85
Cadd	Benign	3.8
Dann	Benign	0.66

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: rs10492785; hg19: chr16-19547357; COSMIC: COSV66816726;