Variant 11-117338552-C-T 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.-21-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,573,528 control chromosomes in the GnomAD database, including 39,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4142 hom., cov: 31)

Exomes 𝑓: 0.22 ( 35334 hom. )

Consequence

CEP164
NM_014956.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.08

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=-0.75).

BP6

Variant 11-117338552-C-T is Benign according to our data. Variant chr11-117338552-C-T is described in ClinVar as [Benign]. Clinvar id is 1245048.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117338552-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP164	NM_014956.5 linkuse as main transcript	c.-21-14C>T		intron_variant		ENST00000278935.8	NP_055771.4	Q9UPV0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP164	ENST00000278935.8 linkuse as main transcript	c.-21-14C>T		intron_variant		1	NM_014956.5	ENSP00000278935.3		Q9UPV0-1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34805

AN:

151942

Hom.:

4134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.224

GnomAD3 exomes

AF:

0.224

AC:

56265

AN:

250640

Hom.:

6760

AF XY:

0.222

AC XY:

30067

AN XY:

135460

show subpopulations

Gnomad AFR exome

AF:

0.274

Gnomad AMR exome

AF:

0.306

Gnomad ASJ exome

AF:

0.264

Gnomad EAS exome

AF:

0.137

Gnomad SAS exome

AF:

0.253

Gnomad FIN exome

AF:

0.148

Gnomad NFE exome

AF:

0.210

Gnomad OTH exome

AF:

0.234

GnomAD4 exome

AF:

0.220

AC:

312453

AN:

1421466

Hom.:

35334

Cov.:

AF XY:

0.220

AC XY:

156266

AN XY:

709676

show subpopulations

Gnomad4 AFR exome

AF:

0.278

Gnomad4 AMR exome

AF:

0.300

Gnomad4 ASJ exome

AF:

0.267

Gnomad4 EAS exome

AF:

0.126

Gnomad4 SAS exome

AF:

0.255

Gnomad4 FIN exome

AF:

0.154

Gnomad4 NFE exome

AF:

0.217

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.229

AC:

34847

AN:

152062

Hom.:

4142

Cov.:

AF XY:

0.225

AC XY:

16754

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.148

Gnomad4 NFE

AF:

0.208

Gnomad4 OTH

AF:

0.222

Alfa

AF:

0.223

Hom.:

808

Bravo

AF:

0.241

Asia WGS

AF:

0.196

AC:

682

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

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