chr19-49010042-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_006666.3(RUVBL2):c.639C>T(p.Arg213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,597,190 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0061 ( 16 hom., cov: 33)
Exomes 𝑓: 0.00064 ( 14 hom. )
Consequence
RUVBL2
NM_006666.3 synonymous
NM_006666.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -8.16
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 19-49010042-C-T is Benign according to our data. Variant chr19-49010042-C-T is described in ClinVar as [Benign]. Clinvar id is 781514.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-8.16 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00605 (922/152300) while in subpopulation AFR AF= 0.0213 (887/41558). AF 95% confidence interval is 0.0202. There are 16 homozygotes in gnomad4. There are 424 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 922 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUVBL2 | NM_006666.3 | c.639C>T | p.Arg213= | synonymous_variant | 8/15 | ENST00000595090.6 | |
RUVBL2 | NM_001321190.2 | c.537C>T | p.Arg179= | synonymous_variant | 8/15 | ||
RUVBL2 | NM_001321191.1 | c.504C>T | p.Arg168= | synonymous_variant | 8/15 | ||
RUVBL2 | NR_135578.2 | n.653C>T | non_coding_transcript_exon_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUVBL2 | ENST00000595090.6 | c.639C>T | p.Arg213= | synonymous_variant | 8/15 | 1 | NM_006666.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00606 AC: 922AN: 152182Hom.: 16 Cov.: 33
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GnomAD3 exomes AF: 0.00154 AC: 361AN: 234028Hom.: 8 AF XY: 0.00113 AC XY: 144AN XY: 127076
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GnomAD4 exome AF: 0.000638 AC: 922AN: 1444890Hom.: 14 Cov.: 37 AF XY: 0.000535 AC XY: 384AN XY: 717734
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GnomAD4 genome AF: 0.00605 AC: 922AN: 152300Hom.: 16 Cov.: 33 AF XY: 0.00569 AC XY: 424AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2018 | - - |
Computational scores
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Name
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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