dbSNP rs200103555: CEP164:c.3216+20_3216+33delCTGGGGGCTGGGGC (chr11-117396185-GCTGGGGGCTGGGGC-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The ENST00000278935.8(CEP164):c.3216+6_3216+19delCTGGGGGCTGGGGC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 1,610,816 control chromosomes in the GnomAD database, including 668 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 37 hom., cov: 28)

Exomes 𝑓: 0.021 ( 631 hom. )

Consequence

CEP164
ENST00000278935.8 splice_region, intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 1.24

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 -16 ACMG points.

BP6

Variant 11-117396185-GCTGGGGGCTGGGGC-G is Benign according to our data. Variant chr11-117396185-GCTGGGGGCTGGGGC-G is described in ClinVar as [Likely_benign]. Clinvar id is 473083.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117396185-GCTGGGGGCTGGGGC-G is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0165 (2506/152054) while in subpopulation NFE AF= 0.0253 (1721/67968). AF 95% confidence interval is 0.0243. There are 37 homozygotes in gnomad4. There are 1183 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 37 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP164	NM_014956.5 link	c.3216+20_3216+33delCTGGGGGCTGGGGC		intron_variant	Intron 25 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.3216+6_3216+19delCTGGGGGCTGGGGC	splice_region_variant, intron_variant	Intron 25 of 32	1	NM_014956.5	ENSP00000278935.3	Q9UPV0-1
CEP164	ENST00000533223.1 link	n.4098+6_4098+19delCTGGGGGCTGGGGC	splice_region_variant, intron_variant	Intron 11 of 15	1
CEP164	ENST00000533675.5 link	n.3443+6_3443+19delCTGGGGGCTGGGGC	splice_region_variant, intron_variant	Intron 19 of 26	2
CEP164	ENST00000533706.5 link	n.2540+6_2540+19delCTGGGGGCTGGGGC	splice_region_variant, intron_variant	Intron 18 of 26	5

Frequencies

GnomAD3 genomes

AF:

0.0165

AC:

2508

AN:

151940

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00435

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0179

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0219

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0253

Gnomad OTH

AF:

0.0159

GnomAD3 exomes

AF:

0.0175

AC:

4316

AN:

247082

Hom.:

AF XY:

0.0172

AC XY:

2323

AN XY:

134672

show subpopulations

Gnomad AFR exome

AF:

0.00354

Gnomad AMR exome

AF:

0.0175

Gnomad ASJ exome

AF:

0.0199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00223

Gnomad FIN exome

AF:

0.0226

Gnomad NFE exome

AF:

0.0250

Gnomad OTH exome

AF:

0.0226

GnomAD4 exome

AF:

0.0208

AC:

30292

AN:

1458762

Hom.:

631

AF XY:

0.0205

AC XY:

14890

AN XY:

725750

show subpopulations

Gnomad4 AFR exome

AF:

0.00332

Gnomad4 AMR exome

AF:

0.0173

Gnomad4 ASJ exome

AF:

0.0211

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00237

Gnomad4 FIN exome

AF:

0.0236

Gnomad4 NFE exome

AF:

0.0236

Gnomad4 OTH exome

AF:

0.0198

GnomAD4 genome

AF:

0.0165

AC:

2506

AN:

152054

Hom.:

Cov.:

AF XY:

0.0159

AC XY:

1183

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.00434

Gnomad4 AMR

AF:

0.0179

Gnomad4 ASJ

AF:

0.0167

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.0219

Gnomad4 NFE

AF:

0.0253

Gnomad4 OTH

AF:

0.0157

Alfa

AF:

0.0215

Hom.:

Bravo

AF:

0.0159

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.0250

EpiControl

AF:

0.0251

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Nephronophthisis 15

Benign:2

Feb 02, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Likely 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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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