rs1290999
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000487861.5(RAD51B):c.1037-31847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,072 control chromosomes in the GnomAD database, including 46,950 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 0.78 ( 46950 hom., cov: 31)
Consequence
RAD51B
ENST00000487861.5 intron
ENST00000487861.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.323
Genes affected
RAD51B (HGNC:9822): (RAD51 paralog B) The protein encoded by this gene is a member of the RAD51 protein family. RAD51 family members are evolutionarily conserved proteins essential for DNA repair by homologous recombination. This protein has been shown to form a stable heterodimer with the family member RAD51C, which further interacts with the other family members, such as RAD51, XRCC2, and XRCC3. Overexpression of this gene was found to cause cell cycle G1 delay and cell apoptosis, which suggested a role of this protein in sensing DNA damage. Rearrangements between this locus and high mobility group AT-hook 2 (HMGA2, GeneID 8091) have been observed in uterine leiomyomata. [provided by RefSeq, Mar 2016]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD51B | NM_001321809.2 | c.1037-23504A>G | intron_variant | ||||
RAD51B | NM_001321810.2 | c.1037-23504A>G | intron_variant | ||||
RAD51B | NM_001321815.1 | c.923-31999A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD51B | ENST00000487270.5 | c.1037-15326A>G | intron_variant | 1 | |||||
RAD51B | ENST00000487861.5 | c.1037-31847A>G | intron_variant | 1 | |||||
RAD51B | ENST00000488612.5 | c.1037-71622A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.780 AC: 118497AN: 151954Hom.: 46900 Cov.: 31
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?
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.780 AC: 118593AN: 152072Hom.: 46950 Cov.: 31 AF XY: 0.775 AC XY: 57598AN XY: 74318
GnomAD4 genome
?
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118593
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31
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57598
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1947
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at