Variant 11-117390772-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_014956.5(CEP164):c.1935-5C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,613,500 control chromosomes in the GnomAD database, including 22,936 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1525 hom., cov: 31)

Exomes 𝑓: 0.17 ( 21411 hom. )

Consequence

CEP164
NM_014956.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0005488

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.655

Variant links:

Genes affected

CEP164 (HGNC:29182): (centrosomal protein 164) This gene encodes a centrosomal protein involved in microtubule organization, DNA damage response, and chromosome segregation. The encoded protein is required for assembly of primary cilia and localizes to mature centrioles. Defects in this gene are a cause of nephronophthisis-related ciliopathies. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

CEP164 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 (BayesDel_noAF=-0.83).

BP6

Variant 11-117390772-C-G is Benign according to our data. Variant chr11-117390772-C-G is described in ClinVar as [Benign]. Clinvar id is 260476.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117390772-C-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP164	NM_014956.5 linkuse as main transcript	c.1935-5C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000278935.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP164	ENST00000278935.8 linkuse as main transcript	c.1935-5C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_014956.5	P1	Q9UPV0-1

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19367

AN:

151866

Hom.:

1524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0332

Gnomad AMI

AF:

0.0973

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.134

GnomAD3 exomes

AF:

0.169

AC:

42588

AN:

251290

Hom.:

4115

AF XY:

0.170

AC XY:

23095

AN XY:

135810

show subpopulations

Gnomad AFR exome

AF:

0.0294

Gnomad AMR exome

AF:

0.263

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.124

Gnomad SAS exome

AF:

0.196

Gnomad FIN exome

AF:

0.145

Gnomad NFE exome

AF:

0.164

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.167

AC:

243902

AN:

1461516

Hom.:

21411

Cov.:

AF XY:

0.168

AC XY:

122187

AN XY:

727086

show subpopulations

Gnomad4 AFR exome

AF:

0.0292

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.197

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.201

Gnomad4 FIN exome

AF:

0.146

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.156

GnomAD4 genome

AF:

0.127

AC:

19371

AN:

151984

Hom.:

1525

Cov.:

AF XY:

0.129

AC XY:

9555

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.0331

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.184

Gnomad4 FIN

AF:

0.138

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.133

Alfa

AF:

0.156

Hom.:

660

Bravo

AF:

0.130

Asia WGS

AF:

0.130

AC:

450

AN:

3478

EpiCase

AF:

0.162

EpiControl

AF:

0.157

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Nephronophthisis 15

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.7

DANN

Benign

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00055

dbscSNV1_RF

Benign

0.070

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