11-117395596-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014956.5(CEP164):c.2963C>G(p.Thr988Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,613,384 control chromosomes in the GnomAD database, including 71,395 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6249 hom., cov: 32)

Exomes 𝑓: 0.30 ( 65146 hom. )

Consequence

CEP164
NM_014956.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.0690

Publications

29 publications found

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 Gene-Disease associations (from GenCC):

ciliopathy
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
nephronophthisis 15
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics, G2P
Senior-Loken syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CEP164 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0029549599).

BP6

Variant 11-117395596-C-G is Benign according to our data. Variant chr11-117395596-C-G is described in ClinVar as Benign. ClinVar VariationId is 260482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP164	NM_014956.5 link	c.2963C>G	p.Thr988Ser	missense_variant	Exon 24 of 33	ENST00000278935.8	NP_055771.4	Q9UPV0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEP164	ENST00000278935.8 link	c.2963C>G	p.Thr988Ser	missense_variant	Exon 24 of 33	1	NM_014956.5	ENSP00000278935.3	Q9UPV0-1
CEP164	ENST00000533223.1 link	n.3845C>G		non_coding_transcript_exon_variant	Exon 10 of 16	1
CEP164	ENST00000533675.5 link	n.3190C>G		non_coding_transcript_exon_variant	Exon 18 of 27	2
CEP164	ENST00000533706.5 link	n.2287C>G		non_coding_transcript_exon_variant	Exon 17 of 27	5

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

43049

AN:

151950

Hom.:

6245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.293

GnomAD2 exomes

AF:

0.273

AC:

68514

AN:

250808

AF XY:

0.277

show subpopulations

Gnomad AFR exome

AF:

0.269

Gnomad AMR exome

AF:

0.147

Gnomad ASJ exome

AF:

0.246

Gnomad EAS exome

AF:

0.273

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.311

Gnomad OTH exome

AF:

0.274

GnomAD4 exome

AF:

0.297

AC:

433911

AN:

1461316

Hom.:

65146

Cov.:

AF XY:

0.296

AC XY:

215237

AN XY:

726916

show subpopulations

African (AFR)

AF:

0.267

AC:

8946

AN:

33462

American (AMR)

AF:

0.159

AC:

7085

AN:

44692

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

6547

AN:

26126

East Asian (EAS)

AF:

0.298

AC:

11820

AN:

39694

South Asian (SAS)

AF:

0.267

AC:

22993

AN:

86154

European-Finnish (FIN)

AF:

0.296

AC:

15787

AN:

53382

Middle Eastern (MID)

AF:

0.287

AC:

1622

AN:

5658

European-Non Finnish (NFE)

AF:

0.307

AC:

341658

AN:

1111796

Other (OTH)

AF:

0.289

AC:

17453

AN:

60352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

17103

34206

51308

68411

85514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11120

22240

33360

44480

55600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.283

AC:

43062

AN:

152068

Hom.:

6249

Cov.:

AF XY:

0.281

AC XY:

20881

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.268

AC:

11108

AN:

41438

American (AMR)

AF:

0.210

AC:

3210

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

933

AN:

3472

East Asian (EAS)

AF:

0.276

AC:

1421

AN:

5152

South Asian (SAS)

AF:

0.268

AC:

1293

AN:

4826

European-Finnish (FIN)

AF:

0.280

AC:

2970

AN:

10592

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.310

AC:

21097

AN:

67982

Other (OTH)

AF:

0.295

AC:

623

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1601

3203

4804

6406

8007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.299

Hom.:

2293

Bravo

AF:

0.275

TwinsUK

AF:

0.299

AC:

1109

ALSPAC

AF:

0.314

AC:

1211

ESP6500AA

AF:

0.267

AC:

1176

ESP6500EA

AF:

0.309

AC:

2658

ExAC

AF:

0.279

AC:

33887

Asia WGS

AF:

0.266

AC:

926

AN:

3478

EpiCase

AF:

0.312

EpiControl

AF:

0.307

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Nephronophthisis 15

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 22, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

May 12, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

CADD

Benign

9.9

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.0094

Eigen

Benign

-0.79

Eigen_PC

Benign

-0.79

FATHMM_MKL

Benign

0.060

LIST_S2

Benign

0.54

MetaRNN

Benign

0.0030

MetaSVM

Benign

-0.96

MutationAssessor

Benign

2.0

PhyloP100

-0.069

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.80

REVEL

Benign

0.013

Sift

Benign

0.16

Sift4G

Benign

0.47

Polyphen

0.0030

Vest4

0.029

MutPred

0.070

Gain of phosphorylation at T988 (P = 0.058);

MPC

0.10

ClinPred

0.0027

GERP RS

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.037

gMVP

0.034

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over