dbSNP rs7191012: CCP110:p.Ala433Ala (chr16-19536968-G-A) – 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.1299G>A(p.Ala433Ala) 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

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0260

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=-0.83).

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_multiple_submitters_no_conflicts, 2 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 rank	MANE	Protein	UniProt
CCP110	NM_001323572.2 link	c.1299G>A	p.Ala433Ala	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.1299G>A	p.Ala433Ala	synonymous_variant	Exon 4 of 14		NM_001323572.2	ENSP00000511625.1		O43303-2

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23251

AN:

152060

Hom.:

1844

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.148

AC XY:

107606

AN XY:

727222

show subpopulations

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.:

AF XY:

0.152

AC XY:

11338

AN XY:

74388

show subpopulations

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: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

-0.83

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

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