rs151170797
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The ENST00000257287.5(CEP135):āc.2755A>Cā(p.Arg919=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00197 in 1,584,730 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0019 ( 2 hom., cov: 32)
Exomes š: 0.0020 ( 5 hom. )
Consequence
CEP135
ENST00000257287.5 synonymous
ENST00000257287.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.59
Genes affected
CEP135 (HGNC:29086): (centrosomal protein 135) This gene encodes a centrosomal protein, which acts as a scaffolding protein during early centriole biogenesis, and is also required for centriole-centriole cohesion during interphase. Mutations in this gene are associated with autosomal recessive primary microcephaly-8. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 4-56011938-A-C is Benign according to our data. Variant chr4-56011938-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 128698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-56011938-A-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00194 (296/152370) while in subpopulation NFE AF= 0.00244 (166/68042). AF 95% confidence interval is 0.00214. There are 2 homozygotes in gnomad4. There are 157 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP135 | NM_025009.5 | c.2755A>C | p.Arg919= | synonymous_variant | 21/26 | ENST00000257287.5 | NP_079285.2 | |
CEP135 | XM_006714055.4 | c.2722A>C | p.Arg908= | synonymous_variant | 21/26 | XP_006714118.1 | ||
CEP135 | XM_005265788.5 | c.1684A>C | p.Arg562= | synonymous_variant | 14/19 | XP_005265845.1 | ||
CEP135 | XM_011534412.2 | c.1225A>C | p.Arg409= | synonymous_variant | 11/16 | XP_011532714.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP135 | ENST00000257287.5 | c.2755A>C | p.Arg919= | synonymous_variant | 21/26 | 1 | NM_025009.5 | ENSP00000257287 | P1 | |
CEP135 | ENST00000506202.1 | n.2705A>C | non_coding_transcript_exon_variant | 14/19 | 1 | |||||
CEP135 | ENST00000706801.1 | n.820A>C | non_coding_transcript_exon_variant | 5/10 |
Frequencies
GnomAD3 genomes AF: 0.00194 AC: 296AN: 152252Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00186 AC: 419AN: 225278Hom.: 2 AF XY: 0.00188 AC XY: 230AN XY: 122348
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GnomAD4 exome AF: 0.00197 AC: 2827AN: 1432360Hom.: 5 Cov.: 31 AF XY: 0.00197 AC XY: 1400AN XY: 712140
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GnomAD4 genome AF: 0.00194 AC: 296AN: 152370Hom.: 2 Cov.: 32 AF XY: 0.00211 AC XY: 157AN XY: 74512
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 30, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2024 | CEP135: BP4, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 27, 2013 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at