rs16924
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006265.3(RAD21):c.-32-331T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 159,790 control chromosomes in the GnomAD database, including 2,630 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2501 hom., cov: 32)
Exomes 𝑓: 0.15 ( 129 hom. )
Consequence
RAD21
NM_006265.3 intron
NM_006265.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.239
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=-0.85).
BP6
?
Variant 8-116867092-A-G is Benign according to our data. Variant chr8-116867092-A-G is described in ClinVar as [Benign]. Clinvar id is 1276593.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD21 | NM_006265.3 | c.-32-331T>C | intron_variant | ENST00000297338.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD21 | ENST00000297338.7 | c.-32-331T>C | intron_variant | 1 | NM_006265.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.164 AC: 24941AN: 151998Hom.: 2499 Cov.: 32
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GnomAD4 exome AF: 0.152 AC: 1168AN: 7674Hom.: 129 AF XY: 0.153 AC XY: 593AN XY: 3872
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GnomAD4 genome ? AF: 0.164 AC: 24963AN: 152116Hom.: 2501 Cov.: 32 AF XY: 0.164 AC XY: 12173AN XY: 74382
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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 | Jul 14, 2018 | - - |
Computational scores
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Name
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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