rs1023497
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_024053.5(CENPM):c.310+721G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 245,594 control chromosomes in the GnomAD database, including 3 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 0.00055 ( 3 hom., cov: 30)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
CENPM
NM_024053.5 intron
NM_024053.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.165
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=-0.81).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000168 (16/95202) while in subpopulation EAS AF= 0.0279 (11/394). AF 95% confidence interval is 0.0157. There are 0 homozygotes in gnomad4_exome. There are 5 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPM | NM_024053.5 | c.310+721G>T | intron_variant | ENST00000215980.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPM | ENST00000215980.10 | c.310+721G>T | intron_variant | 1 | NM_024053.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000552 AC: 83AN: 150312Hom.: 3 Cov.: 30
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GnomAD4 exome AF: 0.000168 AC: 16AN: 95202Hom.: 0 AF XY: 0.000109 AC XY: 5AN XY: 45698
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GnomAD4 genome ? AF: 0.000552 AC: 83AN: 150392Hom.: 3 Cov.: 30 AF XY: 0.000682 AC XY: 50AN XY: 73292
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ClinVar
Not reported inComputational scores
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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