chr19-49010048-C-T

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.15
Variant links:
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 -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
RUVBL2NM_006666.3 linkuse as main transcriptc.645C>T p.Tyr215= synonymous_variant 8/15 ENST00000595090.6
RUVBL2NM_001321190.2 linkuse as main transcriptc.543C>T p.Tyr181= synonymous_variant 8/15
RUVBL2NM_001321191.1 linkuse as main transcriptc.510C>T p.Tyr170= synonymous_variant 8/15
RUVBL2NR_135578.2 linkuse as main transcriptn.659C>T non_coding_transcript_exon_variant 8/15

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RUVBL2ENST00000595090.6 linkuse as main transcriptc.645C>T p.Tyr215= synonymous_variant 8/151 NM_006666.3 P1Q9Y230-1

Frequencies

GnomAD3 genomes
AF:
0.000513
AC:
78
AN:
152194
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000217
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000970
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000438
AC:
103
AN:
235326
Hom.:
0
AF XY:
0.000453
AC XY:
58
AN XY:
128008
show subpopulations
Gnomad AFR exome
AF:
0.000197
Gnomad AMR exome
AF:
0.0000619
Gnomad ASJ exome
AF:
0.000117
Gnomad EAS exome
AF:
0.0000569
Gnomad SAS exome
AF:
0.000141
Gnomad FIN exome
AF:
0.000195
Gnomad NFE exome
AF:
0.000812
Gnomad OTH exome
AF:
0.000178
GnomAD4 exome
AF:
0.000475
AC:
687
AN:
1447024
Hom.:
0
Cov.:
37
AF XY:
0.000508
AC XY:
365
AN XY:
719166
show subpopulations
Gnomad4 AFR exome
AF:
0.000121
Gnomad4 AMR exome
AF:
0.0000703
Gnomad4 ASJ exome
AF:
0.0000806
Gnomad4 EAS exome
AF:
0.0000505
Gnomad4 SAS exome
AF:
0.0000830
Gnomad4 FIN exome
AF:
0.000249
Gnomad4 NFE exome
AF:
0.000581
Gnomad4 OTH exome
AF:
0.000218
GnomAD4 genome
AF:
0.000506
AC:
77
AN:
152312
Hom.:
0
Cov.:
33
AF XY:
0.000483
AC XY:
36
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.000192
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.000970
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000743
Hom.:
0
Bravo
AF:
0.000423

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenDec 01, 2022RUVBL2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
0.19
DANN
Benign
0.64
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs138614683; hg19: chr19-49513305; API