11-117412084-G-T
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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
NM_014956.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.18
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]
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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 |
---|---|---|---|---|---|---|---|---|
CEP164 | NM_014956.5 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
CEP164 | ENST00000278935.8 | c.4299G>T | p.Ser1433= | synonymous_variant | 33/33 | 1 | NM_014956.5 | ENSP00000278935 | P1 |
Frequencies
GnomAD3 genomes AF: 0.954 AC: 145170AN: 152156Hom.: 69383 Cov.: 32
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GnomAD3 exomes AF: 0.936 AC: 235225AN: 251424Hom.: 110384 AF XY: 0.936 AC XY: 127123AN XY: 135882
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GnomAD4 exome AF: 0.960 AC: 1403704AN: 1461822Hom.: 674898 Cov.: 53 AF XY: 0.958 AC XY: 696691AN XY: 727222
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GnomAD4 genome AF: 0.954 AC: 145286AN: 152274Hom.: 69441 Cov.: 32 AF XY: 0.951 AC XY: 70823AN XY: 74438
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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 submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Nephronophthisis 15 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at