rs753307
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006666.3(RUVBL2):c.1251+77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 1,549,206 control chromosomes in the GnomAD database, including 187,036 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 0.47 ( 17177 hom., cov: 33)
Exomes 𝑓: 0.49 ( 169859 hom. )
Consequence
RUVBL2
NM_006666.3 intron
NM_006666.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.386
Genes affected
RUVBL2 (HGNC:10475): (RuvB like AAA ATPase 2) This gene encodes the second human homologue of the bacterial RuvB gene. Bacterial RuvB protein is a DNA helicase essential for homologous recombination and DNA double-strand break repair. Functional analysis showed that this gene product has both ATPase and DNA helicase activities. This gene is physically linked to the CGB/LHB gene cluster on chromosome 19q13.3, and is very close (55 nt) to the LHB gene, in the opposite orientation. [provided by RefSeq, Jul 2008]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUVBL2 | NM_006666.3 | c.1251+77C>T | intron_variant | ENST00000595090.6 | |||
RUVBL2 | NM_001321190.2 | c.1149+77C>T | intron_variant | ||||
RUVBL2 | NM_001321191.1 | c.1116+77C>T | intron_variant | ||||
RUVBL2 | NR_135578.2 | n.1265+77C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUVBL2 | ENST00000595090.6 | c.1251+77C>T | intron_variant | 1 | NM_006666.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.471 AC: 71582AN: 151960Hom.: 17162 Cov.: 33
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GnomAD4 exome AF: 0.490 AC: 685028AN: 1397128Hom.: 169859 Cov.: 26 AF XY: 0.490 AC XY: 339500AN XY: 692646
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GnomAD4 genome ? AF: 0.471 AC: 71622AN: 152078Hom.: 17177 Cov.: 33 AF XY: 0.472 AC XY: 35074AN XY: 74322
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at