chr5-42769545-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134848.2(CCDC152):c.194-52T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,411,194 control chromosomes in the GnomAD database, including 50,444 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 4520 hom., cov: 32)
Exomes 𝑓: 0.27 ( 45924 hom. )
Consequence
CCDC152
NM_001134848.2 intron
NM_001134848.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.60
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC152 | NM_001134848.2 | c.194-52T>C | intron_variant | ENST00000361970.10 | |||
CCDC152 | XM_047416584.1 | c.257-52T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC152 | ENST00000361970.10 | c.194-52T>C | intron_variant | 1 | NM_001134848.2 | P1 | |||
CCDC152 | ENST00000388827.4 | c.194-52T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.219 AC: 33189AN: 151852Hom.: 4510 Cov.: 32
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GnomAD4 exome AF: 0.265 AC: 334095AN: 1259224Hom.: 45924 AF XY: 0.263 AC XY: 162915AN XY: 618326
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GnomAD4 genome ? AF: 0.219 AC: 33227AN: 151970Hom.: 4520 Cov.: 32 AF XY: 0.222 AC XY: 16508AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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