rs6425793
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024296.5(CCDC28B):c.164+728A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 155,446 control chromosomes in the GnomAD database, including 4,410 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 0.21 ( 4286 hom., cov: 32)
Exomes 𝑓: 0.27 ( 124 hom. )
Consequence
CCDC28B
NM_024296.5 intron
NM_024296.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.243
Genes affected
CCDC28B (HGNC:28163): (coiled-coil domain containing 28B) The product of this gene localizes to centrosomes and basal bodies. The protein colocalizes with several proteins associated with Bardet-Biedl syndrome (BBS) and participates in the regulation of cilia development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC28B | NM_024296.5 | c.164+728A>G | intron_variant | ENST00000373602.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC28B | ENST00000373602.10 | c.164+728A>G | intron_variant | 1 | NM_024296.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.214 AC: 32529AN: 152086Hom.: 4285 Cov.: 32
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GnomAD4 exome AF: 0.273 AC: 886AN: 3242Hom.: 124 Cov.: 0 AF XY: 0.268 AC XY: 470AN XY: 1752
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GnomAD4 genome ? AF: 0.214 AC: 32536AN: 152204Hom.: 4286 Cov.: 32 AF XY: 0.211 AC XY: 15737AN XY: 74410
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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