Variant chr8-96231492-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006294.5(UQCRB):c.258+282C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,532,672 control chromosomes in the GnomAD database, including 105,241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 8188 hom., cov: 33)

Exomes 𝑓: 0.37 ( 97053 hom. )

Consequence

UQCRB
NM_006294.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.311

Variant links:

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]

UQCRB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 8-96231492-G-A is Benign according to our data. Variant chr8-96231492-G-A is described in ClinVar as [Benign]. Clinvar id is 1246446.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
UQCRB	NM_006294.5 linkuse as main transcript	c.258+282C>T		intron_variant		ENST00000287022.10
UQCRB	NM_001254752.2 linkuse as main transcript	c.282C>T	p.His94=	synonymous_variant	4/5
UQCRB	NM_001199975.3 linkuse as main transcript	c.162+282C>T		intron_variant
UQCRB	NR_045639.2 linkuse as main transcript	n.297C>T		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRB	ENST00000287022.10 linkuse as main transcript	c.258+282C>T		intron_variant		1	NM_006294.5	P1	P14927-1

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46852

AN:

152074

Hom.:

8185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.305

GnomAD3 exomes

AF:

0.324

AC:

41849

AN:

129318

Hom.:

7327

AF XY:

0.333

AC XY:

23495

AN XY:

70546

show subpopulations

Gnomad AFR exome

AF:

0.150

Gnomad AMR exome

AF:

0.261

Gnomad ASJ exome

AF:

0.309

Gnomad EAS exome

AF:

0.178

Gnomad SAS exome

AF:

0.343

Gnomad FIN exome

AF:

0.431

Gnomad NFE exome

AF:

0.390

Gnomad OTH exome

AF:

0.341

GnomAD4 exome

AF:

0.370

AC:

511365

AN:

1380480

Hom.:

97053

Cov.:

AF XY:

0.371

AC XY:

252684

AN XY:

681098

show subpopulations

Gnomad4 AFR exome

AF:

0.141

Gnomad4 AMR exome

AF:

0.263

Gnomad4 ASJ exome

AF:

0.312

Gnomad4 EAS exome

AF:

0.190

Gnomad4 SAS exome

AF:

0.342

Gnomad4 FIN exome

AF:

0.422

Gnomad4 NFE exome

AF:

0.390

Gnomad4 OTH exome

AF:

0.341

GnomAD4 genome

AF:

0.308

AC:

46859

AN:

152192

Hom.:

8188

Cov.:

AF XY:

0.309

AC XY:

22991

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.334

Gnomad4 EAS

AF:

0.188

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.396

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.360

Hom.:

1966

Bravo

AF:

0.289

Asia WGS

AF:

0.265

AC:

924

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -

Mitochondrial complex III deficiency nuclear type 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.9

DANN

Benign

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over