19-49011063-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_006666.3(RUVBL2):c.852C>T(p.Arg284=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000811 in 1,608,224 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0046 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00042 ( 6 hom. )
Consequence
RUVBL2
NM_006666.3 synonymous
NM_006666.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.96
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 19-49011063-C-T is Benign according to our data. Variant chr19-49011063-C-T is described in ClinVar as [Benign]. Clinvar id is 709500.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.96 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00463 (692/149388) while in subpopulation AFR AF= 0.0165 (670/40712). AF 95% confidence interval is 0.0154. There are 6 homozygotes in gnomad4. There are 332 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 684 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUVBL2 | NM_006666.3 | c.852C>T | p.Arg284= | synonymous_variant | 10/15 | ENST00000595090.6 | |
RUVBL2 | NM_001321190.2 | c.750C>T | p.Arg250= | synonymous_variant | 10/15 | ||
RUVBL2 | NM_001321191.1 | c.717C>T | p.Arg239= | synonymous_variant | 10/15 | ||
RUVBL2 | NR_135578.2 | n.866C>T | non_coding_transcript_exon_variant | 10/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUVBL2 | ENST00000595090.6 | c.852C>T | p.Arg284= | synonymous_variant | 10/15 | 1 | NM_006666.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00458 AC: 684AN: 149282Hom.: 6 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
684
AN:
149282
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00108 AC: 267AN: 246530Hom.: 4 AF XY: 0.000859 AC XY: 115AN XY: 133850
GnomAD3 exomes
AF:
AC:
267
AN:
246530
Hom.:
AF XY:
AC XY:
115
AN XY:
133850
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000420 AC: 612AN: 1458836Hom.: 6 Cov.: 34 AF XY: 0.000379 AC XY: 275AN XY: 725590
GnomAD4 exome
AF:
AC:
612
AN:
1458836
Hom.:
Cov.:
34
AF XY:
AC XY:
275
AN XY:
725590
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00463 AC: 692AN: 149388Hom.: 6 Cov.: 32 AF XY: 0.00456 AC XY: 332AN XY: 72842
GnomAD4 genome
?
AF:
AC:
692
AN:
149388
Hom.:
Cov.:
32
AF XY:
AC XY:
332
AN XY:
72842
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
4
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 | Jul 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at