rs16888927
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006265.3(RAD21):c.688+46T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,525,326 control chromosomes in the GnomAD database, including 64,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.22 ( 4466 hom., cov: 33)
Exomes 𝑓: 0.29 ( 60482 hom. )
Consequence
RAD21
NM_006265.3 intron
NM_006265.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0830
Genes affected
RAD21 (HGNC:9811): (RAD21 cohesin complex component) The protein encoded by this gene is highly similar to the gene product of Schizosaccharomyces pombe rad21, a gene involved in the repair of DNA double-strand breaks, as well as in chromatid cohesion during mitosis. This protein is a nuclear phospho-protein, which becomes hyperphosphorylated in cell cycle M phase. The highly regulated association of this protein with mitotic chromatin specifically at the centromere region suggests its role in sister chromatid cohesion in mitotic cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 8-116857221-A-G is Benign according to our data. Variant chr8-116857221-A-G is described in ClinVar as [Benign]. Clinvar id is 675063.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD21 | NM_006265.3 | c.688+46T>C | intron_variant | ENST00000297338.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD21 | ENST00000297338.7 | c.688+46T>C | intron_variant | 1 | NM_006265.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.218 AC: 33206AN: 152064Hom.: 4465 Cov.: 33
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GnomAD3 exomes AF: 0.274 AC: 64022AN: 233322Hom.: 10203 AF XY: 0.290 AC XY: 36605AN XY: 126036
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GnomAD4 exome AF: 0.288 AC: 395024AN: 1373142Hom.: 60482 Cov.: 21 AF XY: 0.294 AC XY: 201279AN XY: 684472
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GnomAD4 genome AF: 0.218 AC: 33217AN: 152184Hom.: 4466 Cov.: 33 AF XY: 0.224 AC XY: 16675AN XY: 74386
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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 | GeneDx | Jun 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational 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