Variant chr16-19536794-G-A 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.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 (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

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

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=0.0015616417).

BP6

Variant 16-19536794-G-A is Benign according to our data. Variant chr16-19536794-G-A is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCP110	NM_001323572.2 linkuse as main transcript	c.1125G>A	p.Met375Ile	missense_variant	4/14	ENST00000694978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCP110	ENST00000694978.1 linkuse as main transcript	c.1125G>A	p.Met375Ile	missense_variant	4/14		NM_001323572.2	P4	O43303-2

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

GnomAD3 exomes

AF:

0.148

AC:

37144

AN:

250300

Hom.:

2901

AF XY:

0.144

AC XY:

19518

AN XY:

135484

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 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:

218810

AN:

1461694

Hom.:

16986

Cov.:

AF XY:

0.148

AC XY:

107581

AN XY:

727130

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.189

Gnomad4 ASJ exome

AF:

0.201

Gnomad4 EAS exome

AF:

0.180

Gnomad4 SAS exome

AF:

0.0853

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.153

AC:

23344

AN:

152180

Hom.:

1858

Cov.:

AF XY:

0.153

AC XY:

11384

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.211

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.0944

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.148

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.150

Hom.:

4371

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

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

0.24

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

.;T;.

Eigen

Uncertain

0.61

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.79

.;T;T

MetaRNN

Benign

0.0016

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.9

M;M;M

MutationTaster

Benign

0.0026

P;P;P

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.4

N;N;N

REVEL

Benign

0.14

Sift

Pathogenic

0.0

D;D;D

Sift4G

Uncertain

0.025

D;D;D

Polyphen

1.0

D;D;D

Vest4

0.26

MutPred

0.24

Gain of methylation at K374 (P = 0.0244);Gain of methylation at K374 (P = 0.0244);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

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