chr19-49010048-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006666.3(RUVBL2):c.645C>T(p.Tyr215=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000478 in 1,599,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00051 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00047 ( 0 hom. )
Consequence
RUVBL2
NM_006666.3 synonymous
NM_006666.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.15
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 19-49010048-C-T is Benign according to our data. Variant chr19-49010048-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650228.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.15 with no splicing effect.
BS2
High AC in GnomAd4 at 77 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUVBL2 | NM_006666.3 | c.645C>T | p.Tyr215= | synonymous_variant | 8/15 | ENST00000595090.6 | |
RUVBL2 | NM_001321190.2 | c.543C>T | p.Tyr181= | synonymous_variant | 8/15 | ||
RUVBL2 | NM_001321191.1 | c.510C>T | p.Tyr170= | synonymous_variant | 8/15 | ||
RUVBL2 | NR_135578.2 | n.659C>T | non_coding_transcript_exon_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUVBL2 | ENST00000595090.6 | c.645C>T | p.Tyr215= | synonymous_variant | 8/15 | 1 | NM_006666.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000513 AC: 78AN: 152194Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000438 AC: 103AN: 235326Hom.: 0 AF XY: 0.000453 AC XY: 58AN XY: 128008
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GnomAD4 exome AF: 0.000475 AC: 687AN: 1447024Hom.: 0 Cov.: 37 AF XY: 0.000508 AC XY: 365AN XY: 719166
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GnomAD4 genome AF: 0.000506 AC: 77AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000483 AC XY: 36AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | RUVBL2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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