chr8-96231599-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006294.5(UQCRB):c.258+175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,324,054 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 23 hom., cov: 33)
Exomes 𝑓: 0.00098 ( 15 hom. )
Consequence
UQCRB
NM_006294.5 intron
NM_006294.5 intron
Scores
14
Clinical Significance
Conservation
PhyloP100: -1.38
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0024357736).
BP6
Variant 8-96231599-G-A is Benign according to our data. Variant chr8-96231599-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1219586.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00998 (1520/152316) while in subpopulation AFR AF= 0.0347 (1443/41574). AF 95% confidence interval is 0.0332. There are 23 homozygotes in gnomad4. There are 698 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UQCRB | NM_006294.5 | c.258+175C>T | intron_variant | ENST00000287022.10 | |||
UQCRB | NM_001199975.3 | c.162+175C>T | intron_variant | ||||
UQCRB | NM_001254752.2 | c.259-84C>T | intron_variant | ||||
UQCRB | NR_045639.2 | n.274-84C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UQCRB | ENST00000287022.10 | c.258+175C>T | intron_variant | 1 | NM_006294.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00999 AC: 1521AN: 152198Hom.: 23 Cov.: 33
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GnomAD3 exomes AF: 0.00217 AC: 307AN: 141598Hom.: 5 AF XY: 0.00169 AC XY: 130AN XY: 76756
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GnomAD4 exome AF: 0.000980 AC: 1148AN: 1171738Hom.: 15 Cov.: 17 AF XY: 0.000813 AC XY: 479AN XY: 589016
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GnomAD4 genome AF: 0.00998 AC: 1520AN: 152316Hom.: 23 Cov.: 33 AF XY: 0.00937 AC XY: 698AN XY: 74496
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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 | GeneDx | Jun 28, 2018 | - - |
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
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
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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