Genetic Variant CCP110:p.Thr122Thr (chr16-19536035-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001323572.2(CCP110):c.366A>G(p.Thr122Thr) 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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.267

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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_multiple_submitters_no_conflicts, 2 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 rank	MANE	Protein	UniProt
CCP110	NM_001323572.2 link	c.366A>G	p.Thr122Thr	synonymous_variant	Exon 4 of 14	ENST00000694978.1	NP_001310501.1	O43303-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCP110	ENST00000694978.1 link	c.366A>G	p.Thr122Thr	synonymous_variant	Exon 4 of 14		NM_001323572.2	ENSP00000511625.1		O43303-2

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21207

AN:

152028

Hom.:

2102

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0940

AC XY:

68331

AN XY:

727010

show subpopulations

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.:

AF XY:

0.143

AC XY:

10673

AN XY:

74388

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over