rs587783424
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001194998.2(CEP152):c.3990-13G>T 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 0.000013 in 1,613,676 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001194998.2 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP152 | NM_001194998.2 | c.3990-13G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000380950.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.3990-13G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001194998.2 | A2 | |||
CEP152 | ENST00000325747.9 | c.3711-13G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
CEP152 | ENST00000399334.7 | c.3822-13G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | P2 | ||||
CEP152 | ENST00000561245.1 | c.69-13G>T | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248758Hom.: 1 AF XY: 0.0000370 AC XY: 5AN XY: 134986
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461600Hom.: 1 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727084
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74274
ClinVar
Submissions by phenotype
Microcephaly 9, primary, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at