rs693147

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.3090-16A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,613,544 control chromosomes in the GnomAD database, including 292,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.60 ( 27686 hom., cov: 32)

Exomes 𝑓: 0.60 ( 264476 hom. )

Consequence

CEP164
NM_014956.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.03

Publications

12 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 (BayesDel_noAF=-0.91).

BP6

Variant 11-117396038-A-C is Benign according to our data. Variant chr11-117396038-A-C is described in ClinVar as Benign. ClinVar VariationId is 260483.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP164	NM_014956.5 link	c.3090-16A>C		intron_variant	Intron 24 of 32	ENST00000278935.8	NP_055771.4	Q9UPV0-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CEP164	ENST00000278935.8 link	c.3090-16A>C	intron_variant	Intron 24 of 32	1	NM_014956.5	ENSP00000278935.3	Q9UPV0-1
CEP164	ENST00000533223.1 link	n.3972-16A>C	intron_variant	Intron 10 of 15	1
CEP164	ENST00000533675.5 link	n.3317-16A>C	intron_variant	Intron 18 of 26	2
CEP164	ENST00000533706.5 link	n.2414-16A>C	intron_variant	Intron 17 of 26	5

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90669

AN:

151832

Hom.:

27648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.648

Gnomad AMI

AF:

0.614

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.488

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.632

Gnomad OTH

AF:

0.602

GnomAD2 exomes

AF:

0.539

AC:

135269

AN:

251188

AF XY:

0.545

show subpopulations

Gnomad AFR exome

AF:

0.651

Gnomad AMR exome

AF:

0.292

Gnomad ASJ exome

AF:

0.554

Gnomad EAS exome

AF:

0.345

Gnomad FIN exome

AF:

0.599

Gnomad NFE exome

AF:

0.628

Gnomad OTH exome

AF:

0.544

GnomAD4 exome

AF:

0.597

AC:

872013

AN:

1461594

Hom.:

264476

Cov.:

AF XY:

0.595

AC XY:

432436

AN XY:

727114

show subpopulations

African (AFR)

AF:

0.651

AC:

21788

AN:

33472

American (AMR)

AF:

0.312

AC:

13935

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.556

AC:

14519

AN:

26130

East Asian (EAS)

AF:

0.388

AC:

15394

AN:

39692

South Asian (SAS)

AF:

0.493

AC:

42495

AN:

86210

European-Finnish (FIN)

AF:

0.594

AC:

31730

AN:

53400

Middle Eastern (MID)

AF:

0.538

AC:

3103

AN:

5764

European-Non Finnish (NFE)

AF:

0.624

AC:

694149

AN:

1111838

Other (OTH)

AF:

0.578

AC:

34900

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

18195

36390

54586

72781

90976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18358

36716

55074

73432

91790

<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:

0.597

AC:

90754

AN:

151950

Hom.:

27686

Cov.:

AF XY:

0.590

AC XY:

43830

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.648

AC:

26867

AN:

41442

American (AMR)

AF:

0.430

AC:

6577

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.571

AC:

1980

AN:

3470

East Asian (EAS)

AF:

0.358

AC:

1837

AN:

5132

South Asian (SAS)

AF:

0.490

AC:

2354

AN:

4808

European-Finnish (FIN)

AF:

0.583

AC:

6150

AN:

10554

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.632

AC:

42969

AN:

67946

Other (OTH)

AF:

0.604

AC:

1276

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1868

3737

5605

7474

9342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

758

1516

2274

3032

3790

<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:

0.614

Hom.:

30563

Bravo

AF:

0.587

Asia WGS

AF:

0.458

AC:

1593

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Mar 29, 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:2

May 10, 2021

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

- -

Nephronophthisis 15

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.50

(source)

DANN

Benign

0.42

PhyloP100

-1.0

Mutation Taster

=100/0

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