Variant 1-93207131-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001378204.1(CCDC18):c.942C>T(p.Asn314Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,502,798 control chromosomes in the GnomAD database, including 24,982 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.19 ( 2915 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22067 hom. )

Consequence

CCDC18
NM_001378204.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.375

Variant links:

Genes affected

CCDC18 (HGNC:30370): (coiled-coil domain containing 18)

CCDC18 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 1-93207131-C-T is Benign according to our data. Variant chr1-93207131-C-T is described in ClinVar as [Benign]. Clinvar id is 3060341.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.375 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC18	NM_001378204.1 linkuse as main transcript	c.942C>T	p.Asn314Asn	synonymous_variant	9/29	ENST00000690025.1	NP_001365133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC18	ENST00000690025.1 linkuse as main transcript	c.942C>T	p.Asn314Asn	synonymous_variant	9/29		NM_001378204.1	ENSP00000510597.1		A0A8I5KWA2

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28282

AN:

151576

Hom.:

2905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.193

GnomAD3 exomes

AF:

0.209

AC:

44515

AN:

212564

Hom.:

5366

AF XY:

0.208

AC XY:

24236

AN XY:

116530

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.361

Gnomad ASJ exome

AF:

0.106

Gnomad EAS exome

AF:

0.314

Gnomad SAS exome

AF:

0.282

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.171

AC:

231437

AN:

1351104

Hom.:

22067

Cov.:

AF XY:

0.174

AC XY:

116950

AN XY:

670312

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.108

Gnomad4 EAS exome

AF:

0.317

Gnomad4 SAS exome

AF:

0.278

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.154

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.187

AC:

28327

AN:

151694

Hom.:

2915

Cov.:

AF XY:

0.191

AC XY:

14139

AN XY:

74120

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.108

Gnomad4 EAS

AF:

0.310

Gnomad4 SAS

AF:

0.273

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.167

Hom.:

3001

Bravo

AF:

0.198

Asia WGS

AF:

0.284

AC:

989

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CCDC18-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

9.3

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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