rs10491805
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001012267.3(CENPP):c.565-26112A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0268 in 152,330 control chromosomes in the GnomAD database, including 333 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 0.027 ( 333 hom., cov: 32)
Consequence
CENPP
NM_001012267.3 intron
NM_001012267.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.512
Genes affected
CENPP (HGNC:32933): (centromere protein P) CENPP is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 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=-0.87).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPP | NM_001012267.3 | c.565-26112A>C | intron_variant | ENST00000375587.8 | |||
CENPP | NM_001286969.1 | c.229-26112A>C | intron_variant | ||||
CENPP | XM_024447543.2 | c.289-26112A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPP | ENST00000375587.8 | c.565-26112A>C | intron_variant | 1 | NM_001012267.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0268 AC: 4073AN: 152212Hom.: 329 Cov.: 32
GnomAD3 genomes
?
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4073
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152212
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0268 AC: 4081AN: 152330Hom.: 333 Cov.: 32 AF XY: 0.0307 AC XY: 2288AN XY: 74486
GnomAD4 genome
?
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AC:
4081
AN:
152330
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32
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2288
AN XY:
74486
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213
AN:
3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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