rs226891

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.756C>G(p.Ile252Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 1,613,540 control chromosomes in the GnomAD database, including 651,781 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.91 ( 62994 hom., cov: 32)

Exomes 𝑓: 0.90 ( 588787 hom. )

Consequence

CCP110
NM_001323572.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.06

Publications

29 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=7.255988E-7).

BP6

Variant 16-19536425-C-G is Benign according to our data. Variant chr16-19536425-C-G is described in ClinVar as [Benign]. Clinvar id is 402512.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCP110	NM_001323572.2 link	c.756C>G	p.Ile252Met	missense_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.756C>G	p.Ile252Met	missense_variant	Exon 4 of 14		NM_001323572.2	ENSP00000511625.1		O43303-2

Frequencies

GnomAD3 genomes

AF:

0.908

AC:

138114

AN:

152170

Hom.:

62942

Cov.:

show subpopulations

Gnomad AFR

AF:

0.951

Gnomad AMI

AF:

0.967

Gnomad AMR

AF:

0.877

Gnomad ASJ

AF:

0.949

Gnomad EAS

AF:

0.779

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.906

Gnomad MID

AF:

0.965

Gnomad NFE

AF:

0.913

Gnomad OTH

AF:

0.905

GnomAD2 exomes

AF:

0.869

AC:

217675

AN:

250590

AF XY:

0.861

show subpopulations

Gnomad AFR exome

AF:

0.952

Gnomad AMR exome

AF:

0.862

Gnomad ASJ exome

AF:

0.948

Gnomad EAS exome

AF:

0.785

Gnomad FIN exome

AF:

0.900

Gnomad NFE exome

AF:

0.914

Gnomad OTH exome

AF:

0.873

GnomAD4 exome

AF:

0.895

AC:

1308305

AN:

1461252

Hom.:

588787

Cov.:

AF XY:

0.889

AC XY:

646020

AN XY:

726922

show subpopulations

African (AFR)

AF:

0.954

AC:

31917

AN:

33466

American (AMR)

AF:

0.864

AC:

38607

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.949

AC:

24797

AN:

26126

East Asian (EAS)

AF:

0.813

AC:

32289

AN:

39692

South Asian (SAS)

AF:

0.674

AC:

58060

AN:

86206

European-Finnish (FIN)

AF:

0.900

AC:

47881

AN:

53216

Middle Eastern (MID)

AF:

0.893

AC:

5148

AN:

5764

European-Non Finnish (NFE)

AF:

0.914

AC:

1016158

AN:

1111710

Other (OTH)

AF:

0.885

AC:

53448

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

7187

14374

21560

28747

35934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21434

42868

64302

85736

107170

<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:

0.908

AC:

138222

AN:

152288

Hom.:

62994

Cov.:

AF XY:

0.903

AC XY:

67247

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.951

AC:

39533

AN:

41560

American (AMR)

AF:

0.877

AC:

13421

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.949

AC:

3296

AN:

3472

East Asian (EAS)

AF:

0.780

AC:

4030

AN:

5168

South Asian (SAS)

AF:

0.648

AC:

3128

AN:

4826

European-Finnish (FIN)

AF:

0.906

AC:

9615

AN:

10614

Middle Eastern (MID)

AF:

0.959

AC:

282

AN:

294

European-Non Finnish (NFE)

AF:

0.913

AC:

62124

AN:

68024

Other (OTH)

AF:

0.903

AC:

1911

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

618

1237

1855

2474

3092

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<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:

0.911

Hom.:

47662

Bravo

AF:

0.912

TwinsUK

AF:

0.920

AC:

3412

ALSPAC

AF:

0.913

AC:

3518

ESP6500AA

AF:

0.948

AC:

4165

ESP6500EA

AF:

0.917

AC:

7888

ExAC

AF:

0.868

AC:

105388

Asia WGS

AF:

0.686

AC:

2386

AN:

3478

EpiCase

AF:

0.914

EpiControl

AF:

0.917

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

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.25

(source)

DANN

Benign

0.55

DEOGEN2

Benign

0.0052

.;T;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.041

.;T;T

MetaRNN

Benign

7.3e-7

T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.0

N;N;N

PhyloP100

-1.1

PrimateAI

Benign

0.23

PROVEAN

Benign

0.32

N;N;N

REVEL

Benign

0.0040

Sift

Benign

0.17

T;T;T

Sift4G

Benign

0.22

T;T;T

Polyphen

0.0080

B;B;B

Vest4

0.015

MPC

0.18

ClinPred

0.0078

GERP RS

-7.8

Varity_R

0.024

gMVP

0.041

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over