rs2643338
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006294.5(UQCRB):c.19+271T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 590,358 control chromosomes in the GnomAD database, including 75,210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.55 ( 25520 hom., cov: 32)
Exomes 𝑓: 0.47 ( 49690 hom. )
Consequence
UQCRB
NM_006294.5 intron
NM_006294.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0310
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 8-96235241-A-G is Benign according to our data. Variant chr8-96235241-A-G is described in ClinVar as [Benign]. Clinvar id is 684319.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UQCRB | NM_006294.5 | c.19+271T>C | intron_variant | ENST00000287022.10 | |||
UQCRB | NM_001199975.3 | c.-192+271T>C | intron_variant | ||||
UQCRB | NM_001254752.2 | c.19+271T>C | intron_variant | ||||
UQCRB | NR_045639.2 | n.34+271T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UQCRB | ENST00000287022.10 | c.19+271T>C | intron_variant | 1 | NM_006294.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.554 AC: 84144AN: 151900Hom.: 25469 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
84144
AN:
151900
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:
GnomAD4 exome AF: 0.468 AC: 205327AN: 438340Hom.: 49690 Cov.: 4 AF XY: 0.469 AC XY: 109082AN XY: 232750
GnomAD4 exome
AF:
AC:
205327
AN:
438340
Hom.:
Cov.:
4
AF XY:
AC XY:
109082
AN XY:
232750
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: 0.554 AC: 84247AN: 152018Hom.: 25520 Cov.: 32 AF XY: 0.548 AC XY: 40677AN XY: 74282
GnomAD4 genome
?
AF:
AC:
84247
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
40677
AN XY:
74282
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:
1371
AN:
3478
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 | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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