11-117409922-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7

The NM_014956.5(CEP164):c.4053G>A(p.Thr1351Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000898 in 1,613,988 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000090 ( 0 hom. )

Consequence

CEP164
NM_014956.5 synonymous

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: -2.01

Publications

0 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: Likely_benign. The variant received -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 11-117409922-G-A is Benign according to our data. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086. Variant chr11-117409922-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 473086.

BP7

Synonymous conserved (PhyloP=-2.01 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP164	NM_014956.5 link	c.4053G>A	p.Thr1351Thr	synonymous_variant	Exon 30 of 33	ENST00000278935.8	NP_055771.4	Q9UPV0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP164	ENST00000278935.8 link	c.4053G>A	p.Thr1351Thr	synonymous_variant	Exon 30 of 33	1	NM_014956.5	ENSP00000278935.3		Q9UPV0-1

Frequencies

GnomAD3 genomes

AF:

0.0000921

AC:

AN:

152002

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000725

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000481

AC:

AN:

249250

AF XY:

0.0000593

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000358

Gnomad OTH exome

AF:

0.000491

GnomAD4 exome

AF:

0.0000896

AC:

131

AN:

1461870

Hom.:

Cov.:

AF XY:

0.000111

AC XY:

AN XY:

727236

show subpopulations

African (AFR)

AF:

0.0000597

AC:

AN:

33480

American (AMR)

AF:

0.0000447

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39700

South Asian (SAS)

AF:

0.0000464

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000103

AC:

115

AN:

1112006

Other (OTH)

AF:

0.000116

AC:

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

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:

0.0000920

AC:

AN:

152118

Hom.:

Cov.:

AF XY:

0.000161

AC XY:

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0000723

AC:

AN:

41498

American (AMR)

AF:

0.00

AC:

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5154

South Asian (SAS)

AF:

0.000415

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10570

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000103

AC:

AN:

68014

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.000116

Hom.:

Bravo

AF:

0.0000831

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.000218

EpiControl

AF:

0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Nephronophthisis 15

Uncertain:1Benign:1

Feb 12, 2024

Fulgent Genetics, Fulgent Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

CEP164-related disorder

Benign:1

Aug 28, 2024

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.10

(source)

DANN

Benign

0.52

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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