Genetic Variant NM_014956.5:c.1482T>C (chr11-117381773-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014956.5(CEP164):c.1482T>C(p.Pro494Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 1,600,984 control chromosomes in the GnomAD database, including 690,587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 65745 hom., cov: 32)

Exomes 𝑓: 0.93 ( 624842 hom. )

Consequence

CEP164
NM_014956.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.912

Publications

16 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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 11-117381773-T-C is Benign according to our data. Variant chr11-117381773-T-C is described in ClinVar as Benign. ClinVar VariationId is 260475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.912 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014956.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CEP164	NM_014956.5	MANE Select	c.1482T>C	p.Pro494Pro	synonymous	Exon 13 of 33	NP_055771.4
CEP164	NM_001440949.1		c.1491T>C	p.Pro497Pro	synonymous	Exon 13 of 33	NP_001427878.1
CEP164	NM_001440950.1		c.1482T>C	p.Pro494Pro	synonymous	Exon 13 of 33	NP_001427879.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CEP164	ENST00000278935.8	TSL:1 MANE Select	c.1482T>C	p.Pro494Pro	synonymous	Exon 13 of 33	ENSP00000278935.3
CEP164	ENST00000533675.5	TSL:2	n.1737T>C		non_coding_transcript_exon	Exon 9 of 27
CEP164	ENST00000533706.5	TSL:5	n.806T>C		non_coding_transcript_exon	Exon 6 of 27

Frequencies

GnomAD3 genomes

AF:

0.928

AC:

141215

AN:

152126

Hom.:

65683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.956

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.892

Gnomad ASJ

AF:

0.886

Gnomad EAS

AF:

0.847

Gnomad SAS

AF:

0.854

Gnomad FIN

AF:

0.950

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.931

Gnomad OTH

AF:

0.915

GnomAD2 exomes

AF:

0.908

AC:

203366

AN:

223894

AF XY:

0.907

show subpopulations

Gnomad AFR exome

AF:

0.956

Gnomad AMR exome

AF:

0.871

Gnomad ASJ exome

AF:

0.882

Gnomad EAS exome

AF:

0.846

Gnomad FIN exome

AF:

0.952

Gnomad NFE exome

AF:

0.931

Gnomad OTH exome

AF:

0.915

GnomAD4 exome

AF:

0.928

AC:

1344930

AN:

1448740

Hom.:

624842

Cov.:

AF XY:

0.926

AC XY:

666561

AN XY:

719464

show subpopulations

African (AFR)

AF:

0.953

AC:

31658

AN:

33204

American (AMR)

AF:

0.874

AC:

37809

AN:

43250

Ashkenazi Jewish (ASJ)

AF:

0.887

AC:

22818

AN:

25738

East Asian (EAS)

AF:

0.869

AC:

34048

AN:

39180

South Asian (SAS)

AF:

0.865

AC:

72584

AN:

83864

European-Finnish (FIN)

AF:

0.954

AC:

49850

AN:

52280

Middle Eastern (MID)

AF:

0.905

AC:

5111

AN:

5646

European-Non Finnish (NFE)

AF:

0.937

AC:

1035932

AN:

1105782

Other (OTH)

AF:

0.922

AC:

55120

AN:

59796

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

5213

10426

15638

20851

26064

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21510

43020

64530

86040

107550

<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:

0.928

AC:

141335

AN:

152244

Hom.:

65745

Cov.:

AF XY:

0.927

AC XY:

68992

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.956

AC:

39732

AN:

41544

American (AMR)

AF:

0.892

AC:

13635

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.886

AC:

3075

AN:

3470

East Asian (EAS)

AF:

0.847

AC:

4374

AN:

5162

South Asian (SAS)

AF:

0.854

AC:

4113

AN:

4816

European-Finnish (FIN)

AF:

0.950

AC:

10086

AN:

10614

Middle Eastern (MID)

AF:

0.908

AC:

267

AN:

294

European-Non Finnish (NFE)

AF:

0.931

AC:

63342

AN:

68030

Other (OTH)

AF:

0.915

AC:

1934

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

515

1031

1546

2062

2577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.930

Hom.:

28372

Bravo

AF:

0.926

Asia WGS

AF:

0.860

AC:

2988

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Nephronophthisis 15

Benign:2

Jul 22, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

May 04, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.0

(source)

DANN

Benign

0.31

PhyloP100

-0.91

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over