9-107312950-G-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002874.5(RAD23B):c.553+1213G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,242 control chromosomes in the GnomAD database, including 65,749 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 0.93 ( 65749 hom., cov: 30)
Consequence
RAD23B
NM_002874.5 intron
NM_002874.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0640
Genes affected
RAD23B (HGNC:9813): (RAD23 homolog B, nucleotide excision repair protein) The protein encoded by this gene is one of two human homologs of Saccharomyces cerevisiae Rad23, a protein involved in the nucleotide excision repair (NER). This protein was found to be a component of the protein complex that specifically complements the NER defect of xeroderma pigmentosum group C (XP-c) cell extracts in vitro. This protein was also shown to interact with, and elevate the nucleotide excision activity of 3-methyladenine-DNA glycosylase (MPG), which suggested a role in DNA damage recognition in base excision repair. This protein contains an N-terminal ubiquitin-like domain, which was reported to interact with 26S proteasome, and thus this protein may be involved in the ubiquitin mediated proteolytic pathway in cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Sep 2011]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD23B | NM_002874.5 | c.553+1213G>T | intron_variant | Intron 5 of 9 | ENST00000358015.8 | NP_002865.1 | ||
RAD23B | NM_001244713.1 | c.490+1213G>T | intron_variant | Intron 5 of 9 | NP_001231642.1 | |||
RAD23B | NM_001244724.2 | c.337+1213G>T | intron_variant | Intron 5 of 9 | NP_001231653.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD23B | ENST00000358015.8 | c.553+1213G>T | intron_variant | Intron 5 of 9 | 1 | NM_002874.5 | ENSP00000350708.3 | |||
RAD23B | ENST00000416373.6 | c.337+1213G>T | intron_variant | Intron 5 of 9 | 1 | ENSP00000405623.2 | ||||
RAD23B | ENST00000457811.1 | c.160+1213G>T | intron_variant | Intron 2 of 3 | 3 | ENSP00000396975.1 |
Frequencies
GnomAD3 genomes AF: 0.928 AC: 141229AN: 152124Hom.: 65697 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.928 AC: 141341AN: 152242Hom.: 65749 Cov.: 30 AF XY: 0.930 AC XY: 69202AN XY: 74436
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3478
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at