15-48738267-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001194998.2(CEP152):āc.5115A>Gā(p.Pro1705Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000479 in 1,613,418 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001194998.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.5115A>G | p.Pro1705Pro | synonymous_variant | Exon 27 of 27 | 1 | NM_001194998.2 | ENSP00000370337.2 | ||
CEP152 | ENST00000399334.7 | c.4947A>G | p.Pro1649Pro | synonymous_variant | Exon 26 of 26 | 1 | ENSP00000382271.3 | |||
CEP152 | ENST00000561245.1 | n.142+3364A>G | intron_variant | Intron 2 of 3 | 2 | ENSP00000453591.1 |
Frequencies
GnomAD3 genomes AF: 0.00253 AC: 385AN: 152192Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000607 AC: 151AN: 248598Hom.: 1 AF XY: 0.000415 AC XY: 56AN XY: 134892
GnomAD4 exome AF: 0.000266 AC: 388AN: 1461108Hom.: 2 Cov.: 31 AF XY: 0.000219 AC XY: 159AN XY: 726786
GnomAD4 genome AF: 0.00253 AC: 385AN: 152310Hom.: 1 Cov.: 32 AF XY: 0.00262 AC XY: 195AN XY: 74486
ClinVar
Submissions by phenotype
Microcephaly 9, primary, autosomal recessive Uncertain:1Benign:1
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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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
not provided Benign:2
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CEP152-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Seckel syndrome 5 Benign:1
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at