15-48738079-A-G
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The ENST00000380950.7(CEP152):c.*170T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0344 in 748,566 control chromosomes in the GnomAD database, including 539 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.035 ( 117 hom., cov: 32)
Exomes 𝑓: 0.034 ( 422 hom. )
Consequence
CEP152
ENST00000380950.7 3_prime_UTR
ENST00000380950.7 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.90
Genes affected
CEP152 (HGNC:29298): (centrosomal protein 152) This gene encodes a protein that is thought to be involved with centrosome function. Mutations in this gene have been associated with primary microcephaly (MCPH4). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]
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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=-0.37).
BP6
Variant 15-48738079-A-G is Benign according to our data. Variant chr15-48738079-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 316405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0349 (5324/152346) while in subpopulation AFR AF= 0.043 (1786/41576). AF 95% confidence interval is 0.0413. There are 117 homozygotes in gnomad4. There are 2502 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 117 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP152 | NM_001194998.2 | c.*170T>C | 3_prime_UTR_variant | 27/27 | ENST00000380950.7 | NP_001181927.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.*170T>C | 3_prime_UTR_variant | 27/27 | 1 | NM_001194998.2 | ENSP00000370337 | A2 | ||
CEP152 | ENST00000561245.1 | c.142+3552T>C | intron_variant, NMD_transcript_variant | 2 | ENSP00000453591 |
Frequencies
GnomAD3 genomes AF: 0.0350 AC: 5329AN: 152228Hom.: 117 Cov.: 32
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GnomAD4 exome AF: 0.0343 AC: 20423AN: 596220Hom.: 422 Cov.: 8 AF XY: 0.0340 AC XY: 10445AN XY: 307158
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GnomAD4 genome AF: 0.0349 AC: 5324AN: 152346Hom.: 117 Cov.: 32 AF XY: 0.0336 AC XY: 2502AN XY: 74496
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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:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Microcephaly 9, primary, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Seckel syndrome 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at