chr1-32202008-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024296.5(CCDC28B):c.73C>T(p.Arg25Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0251 in 1,613,614 control chromosomes in the GnomAD database, including 754 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.036 ( 141 hom., cov: 32)
Exomes 𝑓: 0.024 ( 613 hom. )
Consequence
CCDC28B
NM_024296.5 missense
NM_024296.5 missense
Scores
1
9
8
Clinical Significance
Conservation
PhyloP100: 4.00
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0036373138).
BP6
Variant 1-32202008-C-T is Benign according to our data. Variant chr1-32202008-C-T is described in ClinVar as [Benign]. Clinvar id is 1271446.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-32202008-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0528 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC28B | NM_024296.5 | c.73C>T | p.Arg25Trp | missense_variant | 2/6 | ENST00000373602.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC28B | ENST00000373602.10 | c.73C>T | p.Arg25Trp | missense_variant | 2/6 | 1 | NM_024296.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0364 AC: 5533AN: 152152Hom.: 140 Cov.: 32
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GnomAD3 exomes AF: 0.0326 AC: 8168AN: 250196Hom.: 190 AF XY: 0.0338 AC XY: 4574AN XY: 135394
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GnomAD4 exome AF: 0.0239 AC: 34912AN: 1461344Hom.: 613 Cov.: 31 AF XY: 0.0247 AC XY: 17976AN XY: 726978
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GnomAD4 genome AF: 0.0363 AC: 5535AN: 152270Hom.: 141 Cov.: 32 AF XY: 0.0379 AC XY: 2823AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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