rs143893793
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_001375405.1(CEP120):c.402C>T(p.Thr134=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000788 in 1,610,818 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 0.00016 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000070 ( 0 hom. )
Consequence
CEP120
NM_001375405.1 synonymous
NM_001375405.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.165
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 -7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 5-123412460-G-A is Benign according to our data. Variant chr5-123412460-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 476167.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.165 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000164 (25/152242) while in subpopulation EAS AF= 0.00212 (11/5184). AF 95% confidence interval is 0.00119. There are 1 homozygotes in gnomad4. There are 9 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.402C>T | p.Thr134= | synonymous_variant | 4/20 | ENST00000306467.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP120 | ENST00000306467.10 | c.402C>T | p.Thr134= | synonymous_variant | 4/20 | 5 | NM_001375405.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152124Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000203 AC: 50AN: 246390Hom.: 0 AF XY: 0.000187 AC XY: 25AN XY: 133824
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GnomAD4 exome AF: 0.0000699 AC: 102AN: 1458576Hom.: 0 Cov.: 30 AF XY: 0.0000606 AC XY: 44AN XY: 725504
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GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152242Hom.: 1 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Short-rib thoracic dysplasia 13 with or without polydactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
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Name
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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