dbSNP rs17227190: CCP110:p.Lys583Lys (chr16-19537418-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001323572.2(CCP110):c.1749A>G(p.Lys583Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 1,613,200 control chromosomes in the GnomAD database, including 4,737 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 360 hom., cov: 33)

Exomes 𝑓: 0.075 ( 4377 hom. )

Consequence

CCP110
NM_001323572.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.57

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 16-19537418-A-G is Benign according to our data. Variant chr16-19537418-A-G is described in ClinVar as [Benign]. Clinvar id is 402515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCP110	NM_001323572.2 link	c.1749A>G	p.Lys583Lys	synonymous_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.1749A>G	p.Lys583Lys	synonymous_variant	Exon 4 of 14		NM_001323572.2	ENSP00000511625.1		O43303-2

Frequencies

GnomAD3 genomes

AF:

0.0629

AC:

9570

AN:

152198

Hom.:

357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0178

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.0949

Gnomad FIN

AF:

0.0873

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0728

Gnomad OTH

AF:

0.0602

GnomAD3 exomes

AF:

0.0819

AC:

20543

AN:

250780

Hom.:

1043

AF XY:

0.0811

AC XY:

10995

AN XY:

135518

show subpopulations

Gnomad AFR exome

AF:

0.0153

Gnomad AMR exome

AF:

0.125

Gnomad ASJ exome

AF:

0.0338

Gnomad EAS exome

AF:

0.129

Gnomad SAS exome

AF:

0.0869

Gnomad FIN exome

AF:

0.0936

Gnomad NFE exome

AF:

0.0712

Gnomad OTH exome

AF:

0.0867

GnomAD4 exome

AF:

0.0747

AC:

109174

AN:

1460884

Hom.:

4377

Cov.:

AF XY:

0.0753

AC XY:

54721

AN XY:

726720

show subpopulations

Gnomad4 AFR exome

AF:

0.0133

Gnomad4 AMR exome

AF:

0.122

Gnomad4 ASJ exome

AF:

0.0340

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.0881

Gnomad4 FIN exome

AF:

0.0930

Gnomad4 NFE exome

AF:

0.0722

Gnomad4 OTH exome

AF:

0.0747

GnomAD4 genome

AF:

0.0628

AC:

9573

AN:

152316

Hom.:

360

Cov.:

AF XY:

0.0639

AC XY:

4757

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.0178

Gnomad4 AMR

AF:

0.100

Gnomad4 ASJ

AF:

0.0320

Gnomad4 EAS

AF:

0.133

Gnomad4 SAS

AF:

0.0948

Gnomad4 FIN

AF:

0.0873

Gnomad4 NFE

AF:

0.0728

Gnomad4 OTH

AF:

0.0591

Alfa

AF:

0.0526

Hom.:

130

Bravo

AF:

0.0632

Asia WGS

AF:

0.110

AC:

382

AN:

3478

EpiCase

AF:

0.0688

EpiControl

AF:

0.0672

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

BayesDel_noAF

Benign

-0.52

CADD

Benign

8.6

DANN

Benign

0.66

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