rs970084
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001384355.1(RAD21L1):c.856+93G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,448,594 control chromosomes in the GnomAD database, including 23,317 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 0.15 ( 1975 hom., cov: 32)
Exomes 𝑓: 0.18 ( 21342 hom. )
Consequence
RAD21L1
NM_001384355.1 intron
NM_001384355.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.215
Genes affected
RAD21L1 (HGNC:16271): (RAD21 cohesin complex component like 1) Predicted to enable chromatin binding activity. Predicted to be involved in mitotic sister chromatid cohesion; replication-born double-strand break repair via sister chromatid exchange; and synaptonemal complex assembly. Predicted to act upstream of or within several processes, including double-strand break repair via homologous recombination; homologous chromosome segregation; and seminiferous tubule development. Predicted to be located in lateral element. Predicted to be part of nuclear meiotic cohesin complex and nuclear mitotic cohesin complex. Predicted to be active in synaptonemal complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD21L1 | NM_001384355.1 | c.856+93G>A | intron_variant | ENST00000683101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD21L1 | ENST00000683101.1 | c.856+93G>A | intron_variant | NM_001384355.1 | A1 | ||||
RAD21L1 | ENST00000409241.5 | c.856+93G>A | intron_variant | 1 | P4 | ||||
RAD21L1 | ENST00000402452.5 | c.856+93G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.152 AC: 23108AN: 152034Hom.: 1975 Cov.: 32
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GnomAD4 exome AF: 0.177 AC: 229000AN: 1296442Hom.: 21342 AF XY: 0.176 AC XY: 111753AN XY: 634854
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GnomAD4 genome ? AF: 0.152 AC: 23115AN: 152152Hom.: 1975 Cov.: 32 AF XY: 0.150 AC XY: 11164AN XY: 74380
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ClinVar
Not reported inComputational 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