rs7772351
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012381.4(ORC3):c.1383-1817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 455,966 control chromosomes in the GnomAD database, including 39,612 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 0.40 ( 12351 hom., cov: 32)
Exomes 𝑓: 0.42 ( 27261 hom. )
Consequence
ORC3
NM_012381.4 intron
NM_012381.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.27
Genes affected
ORC3 (HGNC:8489): (origin recognition complex subunit 3) 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. Studies of a similar gene in Drosophila suggested a possible role of this protein in neuronal proliferation and olfactory memory. Alternatively spliced transcript variants encoding distinct isoforms have been reported for this gene. [provided by RefSeq, Jul 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 = 0.473 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ORC3 | NM_012381.4 | c.1383-1817G>A | intron_variant | ENST00000392844.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ORC3 | ENST00000392844.8 | c.1383-1817G>A | intron_variant | 1 | NM_012381.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.401 AC: 60946AN: 151896Hom.: 12331 Cov.: 32
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GnomAD3 exomes AF: 0.432 AC: 55426AN: 128352Hom.: 12269 AF XY: 0.428 AC XY: 30061AN XY: 70296
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GnomAD4 exome AF: 0.418 AC: 127192AN: 303952Hom.: 27261 Cov.: 0 AF XY: 0.418 AC XY: 72403AN XY: 173068
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GnomAD4 genome ? AF: 0.401 AC: 60998AN: 152014Hom.: 12351 Cov.: 32 AF XY: 0.402 AC XY: 29884AN XY: 74274
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at