Variant chr16-19536425-C-G 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.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. 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 same amino acid change has been previously reported as Likely benignin UniProt.

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

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=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/exons	MANE	UniProt
CCP110	NM_001323572.2 linkuse as main transcript	c.756C>G	p.Ile252Met	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.756C>G	p.Ile252Met	missense_variant	4/14		NM_001323572.2	P4	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

GnomAD3 exomes

AF:

0.869

AC:

217675

AN:

250590

Hom.:

95625

AF XY:

0.861

AC XY:

116634

AN XY:

135540

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 SAS exome

AF:

0.665

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

Gnomad4 AFR exome

AF:

0.954

Gnomad4 AMR exome

AF:

0.864

Gnomad4 ASJ exome

AF:

0.949

Gnomad4 EAS exome

AF:

0.813

Gnomad4 SAS exome

AF:

0.674

Gnomad4 FIN exome

AF:

0.900

Gnomad4 NFE exome

AF:

0.914

Gnomad4 OTH exome

AF:

0.885

GnomAD4 genome

AF:

0.908

AC:

138222

AN:

152288

Hom.:

62994

Cov.:

AF XY:

0.903

AC XY:

67247

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.951

Gnomad4 AMR

AF:

0.877

Gnomad4 ASJ

AF:

0.949

Gnomad4 EAS

AF:

0.780

Gnomad4 SAS

AF:

0.648

Gnomad4 FIN

AF:

0.906

Gnomad4 NFE

AF:

0.913

Gnomad4 OTH

AF:

0.903

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

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

0.056

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.25

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

MutationTaster

Benign

1.0

P;P;P

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

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

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