rs3752591
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000215980.10(CENPM):c.402+98T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,028,960 control chromosomes in the GnomAD database, including 27,154 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 0.24 ( 4651 hom., cov: 32)
Exomes 𝑓: 0.21 ( 22503 hom. )
Consequence
CENPM
ENST00000215980.10 intron
ENST00000215980.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.06
Genes affected
CENPM (HGNC:18352): (centromere protein M) The protein encoded by this gene is an inner protein of the kinetochore, the multi-protein complex that binds spindle microtubules to regulate chromosome segregation during cell division. It belongs to the constitutive centromere-associated network protein group, whose members interact with outer kinetochore proteins and help to maintain centromere identity at each cell division cycle. The protein is structurally related to GTPases but cannot bind guanosine triphosphate. A point mutation that affects interaction with another constitutive centromere-associated network protein, CENP-I, impairs kinetochore assembly and chromosome alignment, suggesting that it is required for kinetochore formation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CENPM | NM_024053.5 | c.402+98T>C | intron_variant | ENST00000215980.10 | NP_076958.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPM | ENST00000215980.10 | c.402+98T>C | intron_variant | 1 | NM_024053.5 | ENSP00000215980 | P1 |
Frequencies
GnomAD3 genomes AF: 0.236 AC: 35819AN: 151974Hom.: 4630 Cov.: 32
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GnomAD4 exome AF: 0.214 AC: 187978AN: 876866Hom.: 22503 AF XY: 0.216 AC XY: 95910AN XY: 443828
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GnomAD4 genome AF: 0.236 AC: 35884AN: 152094Hom.: 4651 Cov.: 32 AF XY: 0.240 AC XY: 17826AN XY: 74374
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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
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at