chr11-117381743-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_014956.5(CEP164):c.1452C>T(p.Pro484Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,609,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000023 ( 0 hom. )

Consequence

CEP164
NM_014956.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.102

Publications

1 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 11-117381743-C-T is Benign according to our data. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117381743-C-T is described in CliVar as Likely_benign. Clinvar id is 540295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.102 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP164	NM_014956.5 link	c.1452C>T	p.Pro484Pro	synonymous_variant	Exon 13 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.1452C>T	p.Pro484Pro	synonymous_variant	Exon 13 of 33	1	NM_014956.5	ENSP00000278935.3	Q9UPV0-1
CEP164	ENST00000533675.5 link	n.1707C>T		non_coding_transcript_exon_variant	Exon 9 of 27	2
CEP164	ENST00000533706.5 link	n.776C>T		non_coding_transcript_exon_variant	Exon 6 of 27	5

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000423

AC:

AN:

236610

AF XY:

0.00000776

show subpopulations

Gnomad AFR exome

AF:

0.0000699

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000226

AC:

AN:

1457544

Hom.:

Cov.:

AF XY:

0.0000207

AC XY:

AN XY:

724666

show subpopulations

African (AFR)

AF:

0.000569

AC:

AN:

33382

American (AMR)

AF:

0.00

AC:

AN:

44358

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25980

East Asian (EAS)

AF:

0.00

AC:

AN:

39562

South Asian (SAS)

AF:

0.00

AC:

AN:

85194

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52992

Middle Eastern (MID)

AF:

0.000177

AC:

AN:

5634

European-Non Finnish (NFE)

AF:

9.01e-7

AC:

AN:

1110264

Other (OTH)

AF:

0.000199

AC:

AN:

60178

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000131

AC:

AN:

152312

Hom.:

Cov.:

AF XY:

0.0000268

AC XY:

AN XY:

74498

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000481

AC:

AN:

41552

American (AMR)

AF:

0.00

AC:

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68028

Other (OTH)

AF:

0.00

AC:

AN:

2112

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.325

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000113

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Nephronophthisis 15

Benign:2

Mar 24, 2022

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 18, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.70

CADD

Benign

5.9

(source)

DANN

Benign

0.56

PhyloP100

0.10

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over