rs201002987
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014956.5(CEP164):c.2427G>A(p.Lys809=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,614,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
CEP164
NM_014956.5 synonymous
NM_014956.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.333
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 11-117392561-G-A is Benign according to our data. Variant chr11-117392561-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 473080.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.333 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP164 | NM_014956.5 | c.2427G>A | p.Lys809= | synonymous_variant | 19/33 | ENST00000278935.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP164 | ENST00000278935.8 | c.2427G>A | p.Lys809= | synonymous_variant | 19/33 | 1 | NM_014956.5 | P1 | |
CEP164 | ENST00000533223.1 | n.3309G>A | non_coding_transcript_exon_variant | 5/16 | 1 | ||||
CEP164 | ENST00000533675.5 | n.2535G>A | non_coding_transcript_exon_variant | 14/27 | 2 | ||||
CEP164 | ENST00000533706.5 | n.1751G>A | non_coding_transcript_exon_variant | 12/27 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251212Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135806
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461856Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727232
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GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Nephronophthisis 15 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2023 | - - |
Computational scores
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Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at