dbSNP rs693147: CEP164:c.3090-16A>C (chr11-117396038-A-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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

GnomAD3 exomes

AF:

0.539

AC:

135269

AN:

251188

Hom.:

38754

AF XY:

0.545

AC XY:

73991

AN XY:

135746

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 SAS exome

AF:

0.493

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

Gnomad4 AFR exome

AF:

0.651

Gnomad4 AMR exome

AF:

0.312

Gnomad4 ASJ exome

AF:

0.556

Gnomad4 EAS exome

AF:

0.388

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.594

Gnomad4 NFE exome

AF:

0.624

Gnomad4 OTH exome

AF:

0.578

GnomAD4 genome

AF:

0.597

AC:

90754

AN:

151950

Hom.:

27686

Cov.:

AF XY:

0.590

AC XY:

43830

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.648

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.490

Gnomad4 FIN

AF:

0.583

Gnomad4 NFE

AF:

0.632

Gnomad4 OTH

AF:

0.604

Alfa

AF:

0.620

Hom.:

24373

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

DANN

Benign

0.42

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over