11-117412084-G-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014956.5(CEP164):​c.4299G>T​(p.Ser1433=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.96 in 1,614,096 control chromosomes in the GnomAD database, including 744,339 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 69441 hom., cov: 32)
Exomes 𝑓: 0.96 ( 674898 hom. )

Consequence

CEP164
NM_014956.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.18
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 11-117412084-G-T is Benign according to our data. Variant chr11-117412084-G-T is described in ClinVar as [Benign]. Clinvar id is 260490.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117412084-G-T is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-1.18 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CEP164NM_014956.5 linkuse as main transcriptc.4299G>T p.Ser1433= synonymous_variant 33/33 ENST00000278935.8 NP_055771.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEP164ENST00000278935.8 linkuse as main transcriptc.4299G>T p.Ser1433= synonymous_variant 33/331 NM_014956.5 ENSP00000278935 P1Q9UPV0-1

Frequencies

GnomAD3 genomes
AF:
0.954
AC:
145170
AN:
152156
Hom.:
69383
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.960
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.913
Gnomad ASJ
AF:
0.936
Gnomad EAS
AF:
0.840
Gnomad SAS
AF:
0.858
Gnomad FIN
AF:
0.981
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.971
Gnomad OTH
AF:
0.951
GnomAD3 exomes
AF:
0.936
AC:
235225
AN:
251424
Hom.:
110384
AF XY:
0.936
AC XY:
127123
AN XY:
135882
show subpopulations
Gnomad AFR exome
AF:
0.961
Gnomad AMR exome
AF:
0.889
Gnomad ASJ exome
AF:
0.929
Gnomad EAS exome
AF:
0.839
Gnomad SAS exome
AF:
0.874
Gnomad FIN exome
AF:
0.979
Gnomad NFE exome
AF:
0.970
Gnomad OTH exome
AF:
0.947
GnomAD4 exome
AF:
0.960
AC:
1403704
AN:
1461822
Hom.:
674898
Cov.:
53
AF XY:
0.958
AC XY:
696691
AN XY:
727222
show subpopulations
Gnomad4 AFR exome
AF:
0.958
Gnomad4 AMR exome
AF:
0.892
Gnomad4 ASJ exome
AF:
0.931
Gnomad4 EAS exome
AF:
0.867
Gnomad4 SAS exome
AF:
0.875
Gnomad4 FIN exome
AF:
0.980
Gnomad4 NFE exome
AF:
0.973
Gnomad4 OTH exome
AF:
0.951
GnomAD4 genome
AF:
0.954
AC:
145286
AN:
152274
Hom.:
69441
Cov.:
32
AF XY:
0.951
AC XY:
70823
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.960
Gnomad4 AMR
AF:
0.913
Gnomad4 ASJ
AF:
0.936
Gnomad4 EAS
AF:
0.840
Gnomad4 SAS
AF:
0.858
Gnomad4 FIN
AF:
0.981
Gnomad4 NFE
AF:
0.971
Gnomad4 OTH
AF:
0.951
Alfa
AF:
0.964
Hom.:
87018
Bravo
AF:
0.951
Asia WGS
AF:
0.865
AC:
3007
AN:
3478
EpiCase
AF:
0.967
EpiControl
AF:
0.966

ClinVar

Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:3
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Benign, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Nephronophthisis 15 Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 22, 2021- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.60
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
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.

Other links and lift over

dbSNP: rs522885; hg19: chr11-117282800; API