rs199783386
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_014956.5(CEP164):c.1409+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000778 in 1,594,850 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00035 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000049 ( 0 hom. )
Consequence
CEP164
NM_014956.5 intron
NM_014956.5 intron
Scores
2
Splicing: ADA: 0.0001117
2
Clinical Significance
Conservation
PhyloP100: -1.96
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 -10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 11-117380715-G-A is Benign according to our data. Variant chr11-117380715-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 473078.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP164 | NM_014956.5 | c.1409+10G>A | intron_variant | ENST00000278935.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP164 | ENST00000278935.8 | c.1409+10G>A | intron_variant | 1 | NM_014956.5 | P1 | |||
CEP164 | ENST00000533675.5 | n.1664+1G>A | splice_donor_variant, non_coding_transcript_variant | 2 | |||||
CEP164 | ENST00000533706.5 | n.733+10G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000355 AC: 54AN: 152210Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000105 AC: 23AN: 219088Hom.: 0 AF XY: 0.0000851 AC XY: 10AN XY: 117556
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GnomAD4 exome AF: 0.0000485 AC: 70AN: 1442640Hom.: 0 Cov.: 30 AF XY: 0.0000433 AC XY: 31AN XY: 715812
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GnomAD4 genome ? AF: 0.000355 AC: 54AN: 152210Hom.: 1 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74362
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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
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 06, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 26, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at