rs7191012

Variant names:

• chr16-19536968-G-A
• rs7191012
• NM_001323572.2:c.1299G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-19536968-G-A
• chr16-19536968-G-T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_001323572.2(CCP110):​c.1299G>A​(p.Ala433Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,614,030 control chromosomes in the GnomAD database, including 18,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (1844 hom., cov: 33)
  • Exomes 𝑓: 0.15 (17002 hom.)
• Consequence: CCP110 NM_001323572.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0260
• Publications: 11 publications found

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 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 16-19536968-G-A is Benign according to our data. Variant chr16-19536968-G-A is described in ClinVar as Benign. ClinVar VariationId is 402514.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.026 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCP110	NM_001323572.2	c.1299G>A	p.Ala433Ala	synonymous_variant	Exon 4 of 14	ENST00000694978.1	NP_001310501.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCP110	ENST00000694978.1	c.1299G>A	p.Ala433Ala	synonymous_variant	Exon 4 of 14		NM_001323572.2	ENSP00000511625.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23251 AN: 152060 Hom.: 1844 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.171

GnomAD2 exomes AF: 0.148 AC: 37289 AN: 251214 AF XY: 0.144

Gnomad AFR exome AF: 0.156

Gnomad AMR exome AF: 0.192

Gnomad ASJ exome AF: 0.206

Gnomad EAS exome AF: 0.155

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.151

Gnomad OTH exome AF: 0.142

GnomAD4 exome AF: 0.150 AC: 218876 AN: 1461852 Hom.: 17002 Cov.: 36 AF XY: 0.148 AC XY: 107606 AN XY: 727222

African (AFR) AF: 0.154 AC: 5152 AN: 33476

American (AMR) AF: 0.189 AC: 8448 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 5258 AN: 26134

East Asian (EAS) AF: 0.179 AC: 7106 AN: 39698

South Asian (SAS) AF: 0.0854 AC: 7362 AN: 86254

European-Finnish (FIN) AF: 0.115 AC: 6135 AN: 53410

Middle Eastern (MID) AF: 0.201 AC: 1159 AN: 5768

European-Non Finnish (NFE) AF: 0.152 AC: 168966 AN: 1111992

Other (OTH) AF: 0.154 AC: 9290 AN: 60396

GnomAD4 genome AF: 0.153 AC: 23257 AN: 152178 Hom.: 1844 Cov.: 33 AF XY: 0.152 AC XY: 11338 AN XY: 74388

African (AFR) AF: 0.155 AC: 6451 AN: 41508

American (AMR) AF: 0.195 AC: 2985 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3470

East Asian (EAS) AF: 0.166 AC: 864 AN: 5194

South Asian (SAS) AF: 0.0944 AC: 456 AN: 4832

European-Finnish (FIN) AF: 0.114 AC: 1201 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10058 AN: 67998

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.156 Hom.: 3207

Bravo AF: 0.162

Asia WGS AF: 0.126 AC: 440 AN: 3478

EpiCase AF: 0.153

EpiControl AF: 0.157

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	-0.83
CADD	Benign	1.6
DANN	Benign	0.37
PhyloP100		0.026
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7191012; hg19: chr16-19548290; COSMIC: COSV66817375; COSMIC: COSV66817375;