rs1127678
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394669.1(CCDC57):c.*71G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,273,680 control chromosomes in the GnomAD database, including 29,503 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 0.23 ( 4212 hom., cov: 34)
Exomes 𝑓: 0.21 ( 25291 hom. )
Consequence
CCDC57
NM_001394669.1 3_prime_UTR
NM_001394669.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.200
Genes affected
CCDC57 (HGNC:27564): (coiled-coil domain containing 57) Involved in several processes, including G2/M transition of mitotic cell cycle; cilium assembly; and microtubule cytoskeleton organization. Located in centriolar satellite; centriole; and spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC57 | NM_001394669.1 | c.*71G>A | 3_prime_UTR_variant | 19/19 | ENST00000694881.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC57 | ENST00000694881.1 | c.*71G>A | 3_prime_UTR_variant | 19/19 | NM_001394669.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.228 AC: 34748AN: 152072Hom.: 4211 Cov.: 34
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GnomAD4 exome AF: 0.206 AC: 230513AN: 1121490Hom.: 25291 Cov.: 15 AF XY: 0.204 AC XY: 115776AN XY: 566294
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GnomAD4 genome AF: 0.228 AC: 34763AN: 152190Hom.: 4212 Cov.: 34 AF XY: 0.224 AC XY: 16633AN XY: 74392
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at