16-19536794-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001323572.2(CCP110):c.1125G>A(p.Met375Ile) variant causes a missense change. The variant allele was found at a frequency of 0.15 in 1,613,874 control chromosomes in the GnomAD database, including 18,844 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1858 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16986 hom. )

Consequence

CCP110
NM_001323572.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.39

Publications

25 publications found

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 Gene-Disease associations (from GenCC):

ciliopathy
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

CCP110 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015616417).

BP6

Variant 16-19536794-G-A is Benign according to our data. Variant chr16-19536794-G-A is described in ClinVar as Benign. ClinVar VariationId is 402513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323572.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CCP110	NM_001323572.2	MANE Select	c.1125G>A	p.Met375Ile	missense	Exon 4 of 14	NP_001310501.1
CCP110	NM_001199022.3		c.1125G>A	p.Met375Ile	missense	Exon 4 of 15	NP_001185951.2
CCP110	NM_001323569.2		c.1125G>A	p.Met375Ile	missense	Exon 5 of 16	NP_001310498.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CCP110	ENST00000694978.1	MANE Select	c.1125G>A	p.Met375Ile	missense	Exon 4 of 14	ENSP00000511625.1
CCP110	ENST00000381396.9	TSL:1	c.1125G>A	p.Met375Ile	missense	Exon 4 of 15	ENSP00000370803.5
CCP110	ENST00000396208.4	TSL:1	c.1125G>A	p.Met375Ile	missense	Exon 3 of 13	ENSP00000379511.2

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23341

AN:

152064

Hom.:

1859

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.0950

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.172

GnomAD2 exomes

AF:

0.148

AC:

37144

AN:

250300

AF XY:

0.144

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.192

Gnomad ASJ exome

AF:

0.205

Gnomad EAS exome

AF:

0.155

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.151

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.150

AC:

218810

AN:

1461694

Hom.:

16986

Cov.:

AF XY:

0.148

AC XY:

107581

AN XY:

727130

show subpopulations

African (AFR)

AF:

0.155

AC:

5200

AN:

33478

American (AMR)

AF:

0.189

AC:

8447

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

5257

AN:

26132

East Asian (EAS)

AF:

0.180

AC:

7136

AN:

39698

South Asian (SAS)

AF:

0.0853

AC:

7354

AN:

86252

European-Finnish (FIN)

AF:

0.115

AC:

6131

AN:

53390

Middle Eastern (MID)

AF:

0.201

AC:

1162

AN:

5768

European-Non Finnish (NFE)

AF:

0.152

AC:

168830

AN:

1111872

Other (OTH)

AF:

0.154

AC:

9293

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

11003

22006

33008

44011

55014

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6094

12188

18282

24376

30470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.153

AC:

23344

AN:

152180

Hom.:

1858

Cov.:

AF XY:

0.153

AC XY:

11384

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.157

AC:

6523

AN:

41508

American (AMR)

AF:

0.196

AC:

2993

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.211

AC:

732

AN:

3470

East Asian (EAS)

AF:

0.168

AC:

868

AN:

5172

South Asian (SAS)

AF:

0.0944

AC:

456

AN:

4828

European-Finnish (FIN)

AF:

0.114

AC:

1203

AN:

10586

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10059

AN:

68000

Other (OTH)

AF:

0.169

AC:

357

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1013

2027

3040

4054

5067

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.152

Hom.:

6211

Bravo

AF:

0.163

TwinsUK

AF:

0.150

AC:

557

ALSPAC

AF:

0.145

AC:

558

ESP6500AA

AF:

0.158

AC:

696

ESP6500EA

AF:

0.156

AC:

1341

ExAC

AF:

0.145

AC:

17594

Asia WGS

AF:

0.126

AC:

440

AN:

3478

EpiCase

AF:

0.153

EpiControl

AF:

0.156

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 v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

Eigen

Uncertain

0.61

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.79

MetaRNN

Benign

0.0016

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.9

PhyloP100

4.4

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.4

REVEL

Benign

0.14

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.025

Polyphen

1.0

Vest4

0.26

MutPred

0.24

Gain of methylation at K374 (P = 0.0244)

MPC

0.68

ClinPred

0.022

GERP RS

4.0

Varity_R

0.76

gMVP

0.10

Mutation Taster

=97/3

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over