rs1497430
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001812.4(CENPC):c.2515+84T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 886,374 control chromosomes in the GnomAD database, including 174,036 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 0.63 ( 30198 hom., cov: 31)
Exomes 𝑓: 0.62 ( 143838 hom. )
Consequence
CENPC
NM_001812.4 intron
NM_001812.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.68
Genes affected
CENPC (HGNC:1854): (centromere protein C) Centromere protein C 1 is a centromere autoantigen and a component of the inner kinetochore plate. The protein is required for maintaining proper kinetochore size and a timely transition to anaphase. A putative pseudogene exists on chromosome 12. [provided by RefSeq, Jul 2008]
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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=-0.76).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPC | NM_001812.4 | c.2515+84T>C | intron_variant | ENST00000273853.11 | |||
CENPC | NM_001362481.2 | c.2491+84T>C | intron_variant | ||||
CENPC | XM_047449526.1 | c.2515+84T>C | intron_variant | ||||
CENPC | NR_155754.2 | n.2781+84T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPC | ENST00000273853.11 | c.2515+84T>C | intron_variant | 1 | NM_001812.4 | P1 | |||
CENPC | ENST00000506882.5 | c.*1239+84T>C | intron_variant, NMD_transcript_variant | 1 | |||||
CENPC | ENST00000515140.1 | c.*167+84T>C | intron_variant, NMD_transcript_variant | 1 | |||||
CENPC | ENST00000513216.5 | c.*167+84T>C | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.628 AC: 95309AN: 151860Hom.: 30152 Cov.: 31
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GnomAD4 exome AF: 0.622 AC: 456675AN: 734396Hom.: 143838 AF XY: 0.624 AC XY: 235386AN XY: 377326
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GnomAD4 genome AF: 0.628 AC: 95401AN: 151978Hom.: 30198 Cov.: 31 AF XY: 0.633 AC XY: 46979AN XY: 74262
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ClinVar
Not reported inComputational scores
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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