chr8-96231112-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006294.5(UQCRB):c.279G>A(p.Pro93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000361 in 1,614,044 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0020 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00019 ( 2 hom. )
Consequence
UQCRB
NM_006294.5 synonymous
NM_006294.5 synonymous
Scores
1
14
Clinical Significance
Conservation
PhyloP100: -0.529
Genes affected
UQCRB (HGNC:12582): (ubiquinol-cytochrome c reductase binding protein) This gene encodes a subunit of the ubiquinol-cytochrome c oxidoreductase complex, which consists of one mitochondrial-encoded and 10 nuclear-encoded subunits. The protein encoded by this gene binds ubiquinone and participates in the transfer of electrons when ubiquinone is bound. This protein plays an important role in hypoxia-induced angiogenesis through mitochondrial reactive oxygen species-mediated signaling. Mutations in this gene are associated with mitochondrial complex III deficiency. Alternatively spliced transcript variants have been found for this gene. Related pseudogenes have been identified on chromosomes 1, 5 and X. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.003632307).
BP6
Variant 8-96231112-C-T is Benign according to our data. Variant chr8-96231112-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 379798.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.529 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UQCRB | NM_006294.5 | c.279G>A | p.Pro93= | synonymous_variant | 4/4 | ENST00000287022.10 | |
UQCRB | NM_001254752.2 | c.416G>A | p.Arg139His | missense_variant | 5/5 | ||
UQCRB | NM_001199975.3 | c.183G>A | p.Pro61= | synonymous_variant | 5/5 | ||
UQCRB | NR_045639.2 | n.584G>A | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UQCRB | ENST00000287022.10 | c.279G>A | p.Pro93= | synonymous_variant | 4/4 | 1 | NM_006294.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00197 AC: 300AN: 152170Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000439 AC: 110AN: 250692Hom.: 1 AF XY: 0.000325 AC XY: 44AN XY: 135538
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GnomAD4 exome AF: 0.000194 AC: 283AN: 1461756Hom.: 2 Cov.: 31 AF XY: 0.000175 AC XY: 127AN XY: 727184
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GnomAD4 genome AF: 0.00197 AC: 300AN: 152288Hom.: 1 Cov.: 33 AF XY: 0.00193 AC XY: 144AN XY: 74466
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
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