rs1491225681
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001375405.1(CEP120):c.1431-10_1431-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 679,596 control chromosomes in the GnomAD database, including 363 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0075 ( 5 hom., cov: 12)
Exomes 𝑓: 0.078 ( 358 hom. )
Consequence
CEP120
NM_001375405.1 splice_polypyrimidine_tract, intron
NM_001375405.1 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.159
Genes affected
CEP120 (HGNC:26690): (centrosomal protein 120) This gene encodes a protein that functions in the microtubule-dependent coupling of the nucleus and the centrosome. A similar protein in mouse plays a role in both interkinetic nuclear migration, which is a characteristic pattern of nuclear movement in neural progenitors, and in neural progenitor self-renewal. Mutations in this gene are predicted to result in neurogenic defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 5-123386675-TTA-T is Benign according to our data. Variant chr5-123386675-TTA-T is described in ClinVar as [Benign]. Clinvar id is 476161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-123386675-TTA-T is described in Lovd as [Benign].
BA1
?
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.1431-10_1431-9del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000306467.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP120 | ENST00000306467.10 | c.1431-10_1431-9del | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001375405.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00748 AC: 375AN: 50158Hom.: 5 Cov.: 12
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GnomAD3 exomes AF: 0.0475 AC: 889AN: 18698Hom.: 130 AF XY: 0.0471 AC XY: 466AN XY: 9904
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GnomAD4 exome AF: 0.0776 AC: 48839AN: 629438Hom.: 358 AF XY: 0.0768 AC XY: 23480AN XY: 305718
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GnomAD4 genome ? AF: 0.00748 AC: 375AN: 50158Hom.: 5 Cov.: 12 AF XY: 0.00823 AC XY: 195AN XY: 23696
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 10, 2019 | - - |
Short-rib thoracic dysplasia 13 with or without polydactyly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at