rs13412430
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006190.5(ORC2):c.*1669A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 25)
Failed GnomAD Quality Control
Consequence
ORC2
NM_006190.5 3_prime_UTR
NM_006190.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.285
Publications
8 publications found
Genes affected
ORC2 (HGNC:8488): (origin recognition complex subunit 2) The origin recognition complex (ORC) is a highly conserved six subunits protein complex essential for the initiation of the DNA replication in eukaryotic cells. Studies in yeast demonstrated that ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors such as Cdc6 and Mcm proteins. The protein encoded by this gene is a subunit of the ORC complex. This protein forms a core complex with ORC3, -4, and -5. It also interacts with CDC45 and MCM10, which are proteins known to be important for the initiation of DNA replication. This protein has been demonstrated to specifically associate with the origin of replication of Epstein-Barr virus in human cells, and is thought to be required for DNA replication from viral origin of replication. Alternatively spliced transcript variants have been found, one of which is a nonsense-mediated mRNA decay candidate. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_006190.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ORC2 | TSL:1 MANE Select | c.*1669A>T | 3_prime_UTR | Exon 18 of 18 | ENSP00000234296.2 | Q13416 | |||
| ORC2 | c.*1669A>T | 3_prime_UTR | Exon 18 of 18 | ENSP00000608789.1 | |||||
| ORC2 | c.*1669A>T | 3_prime_UTR | Exon 17 of 17 | ENSP00000549194.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 142260Hom.: 0 Cov.: 25
GnomAD3 genomes
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25
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GnomAD4 exome Cov.: 0
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GnomAD4 genome 0.00 AC: 0AN: 142260Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 68080
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
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142260
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25
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68080
African (AFR)
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39282
American (AMR)
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12706
Ashkenazi Jewish (ASJ)
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3424
East Asian (EAS)
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4696
South Asian (SAS)
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4468
European-Finnish (FIN)
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8504
Middle Eastern (MID)
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282
European-Non Finnish (NFE)
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66094
Other (OTH)
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1916
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
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Calibrated prediction
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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
Publications
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