1-32204735-T-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000421922.6(CCDC28B):āc.663T>Gā(p.Pro221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,613,838 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00083 ( 1 hom., cov: 32)
Exomes š: 0.0012 ( 1 hom. )
Consequence
CCDC28B
ENST00000421922.6 synonymous
ENST00000421922.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.33
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 1-32204735-T-G is Benign according to our data. Variant chr1-32204735-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 1694505.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.33 with no splicing effect.
BS2
High AC in GnomAd4 at 126 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC28B | NM_024296.5 | c.548+115T>G | intron_variant | ENST00000373602.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC28B | ENST00000373602.10 | c.548+115T>G | intron_variant | 1 | NM_024296.5 | P1 | |||
ENST00000373604.4 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000828 AC: 126AN: 152196Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000795 AC: 199AN: 250316Hom.: 1 AF XY: 0.000768 AC XY: 104AN XY: 135362
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GnomAD4 exome AF: 0.00120 AC: 1758AN: 1461642Hom.: 1 Cov.: 32 AF XY: 0.00113 AC XY: 818AN XY: 727106
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GnomAD4 genome AF: 0.000828 AC: 126AN: 152196Hom.: 1 Cov.: 32 AF XY: 0.000686 AC XY: 51AN XY: 74362
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | CCDC28B: BP4, BP7 - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at