2-24821506-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001322101.2(CENPO):c.*2188G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000227 in 1,613,590 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
CENPO
NM_001322101.2 3_prime_UTR
NM_001322101.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.540
Genes affected
CENPO (HGNC:28152): (centromere protein O) This gene encodes a component of the interphase centromere complex. The encoded protein is localized to the centromere throughout the cell cycle and is required for bipolar spindle assembly, chromosome segregation and checkpoint signaling during mitosis. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]
ADCY3 (HGNC:234): (adenylate cyclase 3) This gene encodes adenylyl cyclase 3 which is a membrane-associated enzyme and catalyzes the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This protein appears to be widely expressed in various human tissues and may be involved in a number of physiological and pathophysiological metabolic processes. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 2-24821506-G-C is Benign according to our data. Variant chr2-24821506-G-C is described in ClinVar as [Benign]. Clinvar id is 1992163.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPO | NM_001322101.2 | c.*2188G>C | 3_prime_UTR_variant | 8/8 | ENST00000380834.7 | ||
ADCY3 | NM_004036.5 | c.3127+11C>G | intron_variant | ENST00000679454.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPO | ENST00000380834.7 | c.*2188G>C | 3_prime_UTR_variant | 8/8 | 5 | NM_001322101.2 | P1 | ||
ADCY3 | ENST00000679454.1 | c.3127+11C>G | intron_variant | NM_004036.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00122 AC: 185AN: 152234Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000271 AC: 68AN: 250626Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135458
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GnomAD4 exome AF: 0.000120 AC: 176AN: 1461238Hom.: 0 Cov.: 30 AF XY: 0.000103 AC XY: 75AN XY: 726938
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | - - |
Computational scores
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Name
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Benign
Cadd
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Benign
RBP_binding_hub_radar
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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