12-913513-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000358495.8(RAD52):c.1196-61T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 1,193,692 control chromosomes in the GnomAD database, including 91,118 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 0.36 ( 10268 hom., cov: 31)
Exomes 𝑓: 0.39 ( 80850 hom. )
Consequence
RAD52
ENST00000358495.8 intron
ENST00000358495.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.873
Genes affected
RAD52 (HGNC:9824): (RAD52 homolog, DNA repair protein) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Rad52, a protein important for DNA double-strand break repair and homologous recombination. This gene product was shown to bind single-stranded DNA ends, and mediate the DNA-DNA interaction necessary for the annealing of complementary DNA strands. It was also found to interact with DNA recombination protein RAD51, which suggested its role in RAD51 related DNA recombination and repair. A pseudogene of this gene is present on chromosome 2. Alternative splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Jul 2014]
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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=-0.62).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD52 | NM_134424.4 | c.1196-61T>C | intron_variant | ENST00000358495.8 | NP_602296.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD52 | ENST00000358495.8 | c.1196-61T>C | intron_variant | 1 | NM_134424.4 | ENSP00000351284 | P2 |
Frequencies
GnomAD3 genomes AF: 0.359 AC: 54542AN: 151896Hom.: 10259 Cov.: 31
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GnomAD4 exome AF: 0.387 AC: 403276AN: 1041678Hom.: 80850 AF XY: 0.384 AC XY: 205917AN XY: 536632
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GnomAD4 genome AF: 0.359 AC: 54575AN: 152014Hom.: 10268 Cov.: 31 AF XY: 0.360 AC XY: 26775AN XY: 74282
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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