Variant rs3751821 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001323572.2(CCP110):c.512C>T(p.Pro171Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,613,600 control chromosomes in the GnomAD database, including 13,971 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.16 ( 2930 hom., cov: 32)

Exomes 𝑓: 0.097 ( 11041 hom. )

Consequence

CCP110
NM_001323572.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.230

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002224356).

BP6

Variant 16-19536181-C-T is Benign according to our data. Variant chr16-19536181-C-T is described in ClinVar as [Benign]. Clinvar id is 402511.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCP110	NM_001323572.2 link	c.512C>T	p.Pro171Leu	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.512C>T	p.Pro171Leu	missense_variant	Exon 4 of 14		NM_001323572.2	ENSP00000511625.1		O43303-2

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24428

AN:

151916

Hom.:

2913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.0726

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0705

Gnomad OTH

AF:

0.146

GnomAD3 exomes

AF:

0.147

AC:

37037

AN:

251278

Hom.:

4598

AF XY:

0.137

AC XY:

18550

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.298

Gnomad AMR exome

AF:

0.289

Gnomad ASJ exome

AF:

0.0556

Gnomad EAS exome

AF:

0.418

Gnomad SAS exome

AF:

0.126

Gnomad FIN exome

AF:

0.0694

Gnomad NFE exome

AF:

0.0695

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.0967

AC:

141351

AN:

1461566

Hom.:

11041

Cov.:

AF XY:

0.0962

AC XY:

69975

AN XY:

727088

show subpopulations

Gnomad4 AFR exome

AF:

0.304

Gnomad4 AMR exome

AF:

0.287

Gnomad4 ASJ exome

AF:

0.0554

Gnomad4 EAS exome

AF:

0.390

Gnomad4 SAS exome

AF:

0.129

Gnomad4 FIN exome

AF:

0.0690

Gnomad4 NFE exome

AF:

0.0713

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.161

AC:

24476

AN:

152034

Hom.:

2930

Cov.:

AF XY:

0.164

AC XY:

12199

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.295

Gnomad4 AMR

AF:

0.225

Gnomad4 ASJ

AF:

0.0490

Gnomad4 EAS

AF:

0.394

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.0726

Gnomad4 NFE

AF:

0.0705

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.0928

Hom.:

2448

Bravo

AF:

0.180

TwinsUK

AF:

0.0769

AC:

285

ALSPAC

AF:

0.0778

AC:

300

ESP6500AA

AF:

0.289

AC:

1269

ESP6500EA

AF:

0.0657

AC:

565

ExAC

AF:

0.142

AC:

17260

Asia WGS

AF:

0.241

AC:

836

AN:

3478

EpiCase

AF:

0.0745

EpiControl

AF:

0.0745

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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 -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.6

DANN

Benign

0.37

DEOGEN2

Benign

0.0085

.;T;.;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.015

LIST_S2

Benign

0.71

.;T;T;T

MetaRNN

Benign

0.0022

T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

-0.71

N;N;N;.

PrimateAI

Benign

0.18

PROVEAN

Benign

-1.2

N;N;N;.

REVEL

Benign

0.037

Sift

Benign

1.0

T;T;T;.

Sift4G

Benign

1.0

T;T;T;T

Polyphen

0.0

B;B;B;.

Vest4

0.024

MPC

0.18

ClinPred

0.00046

GERP RS

-2.3

Varity_R

0.019

gMVP

0.069

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