rs17227190

chr16-19537418-A-Gchr16-19537418-A-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_001323572.2(CCP110):c.1749A>G(p.Lys583=) 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.57

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]

ACMG classification

Verdict is Benign. Variant got -15 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_single_submitter, 1 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/exons	MANE	UniProt
CCP110	NM_001323572.2	c.1749A>G	p.Lys583=	synonymous_variant	4/14	ENST00000694978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCP110	ENST00000694978.1	c.1749A>G	p.Lys583=	synonymous_variant	4/14		NM_001323572.2	P4

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9570 AN: 152198 Hom.: 357 Cov.: 33

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

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.: 32 AF XY: 0.0753 AC XY: 54721 AN XY: 726720

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.: 33 AF XY: 0.0639 AC XY: 4757 AN XY: 74482

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:1

Revision: criteria provided, single submitter

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 -

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

Other links and lift over

dbSNP: rs17227190; hg19: chr16-19548740; COSMIC: COSV66817039; COSMIC: COSV66817039;