Variant 8-96231296-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_006294.5(UQCRB):c.259-165dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00519 in 1,554,954 control chromosomes in the GnomAD database, including 182 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.012 ( 41 hom., cov: 33)

Exomes 𝑓: 0.0045 ( 141 hom. )

Consequence

UQCRB
NM_006294.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.900

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 -10 ACMG points.

BP6

Variant 8-96231296-G-GT is Benign according to our data. Variant chr8-96231296-G-GT is described in ClinVar as [Benign]. Clinvar id is 1234097.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0118 (1796/152362) while in subpopulation EAS AF= 0.0547 (284/5190). AF 95% confidence interval is 0.0495. There are 41 homozygotes in gnomad4. There are 929 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 41 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
UQCRB	NM_006294.5 link	c.259-165dupA	intron_variant		ENST00000287022.10	NP_006285.1	P14927-1
UQCRB	NM_001254752.2 link	c.395+82dupA	intron_variant			NP_001241681.1	P14927-2
UQCRB	NM_001199975.3 link	c.163-165dupA	intron_variant			NP_001186904.1	P14927
UQCRB	NR_045639.2 link	n.492dupA	non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCRB	ENST00000287022.10 link	c.259-165dupA		intron_variant		1	NM_006294.5	ENSP00000287022.5		P14927-1

Frequencies

GnomAD3 genomes

AF:

0.0118

AC:

1795

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0286

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00458

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.0552

Gnomad SAS

AF:

0.0436

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000338

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.0121

AC:

1812

AN:

149700

Hom.:

AF XY:

0.0137

AC XY:

1108

AN XY:

81156

show subpopulations

Gnomad AFR exome

AF:

0.0303

Gnomad AMR exome

AF:

0.00241

Gnomad ASJ exome

AF:

0.00168

Gnomad EAS exome

AF:

0.0546

Gnomad SAS exome

AF:

0.0360

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000242

Gnomad OTH exome

AF:

0.00346

GnomAD4 exome

AF:

0.00447

AC:

6273

AN:

1402592

Hom.:

141

Cov.:

AF XY:

0.00530

AC XY:

3672

AN XY:

692648

show subpopulations

Gnomad4 AFR exome

AF:

0.0310

Gnomad4 AMR exome

AF:

0.00283

Gnomad4 ASJ exome

AF:

0.00154

Gnomad4 EAS exome

AF:

0.0449

Gnomad4 SAS exome

AF:

0.0353

Gnomad4 FIN exome

AF:

0.0000209

Gnomad4 NFE exome

AF:

0.000230

Gnomad4 OTH exome

AF:

0.00705

GnomAD4 genome

AF:

0.0118

AC:

1796

AN:

152362

Hom.:

Cov.:

AF XY:

0.0125

AC XY:

929

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.0285

Gnomad4 AMR

AF:

0.00457

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.0547

Gnomad4 SAS

AF:

0.0441

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000338

Gnomad4 OTH

AF:

0.00757

Alfa

AF:

0.00360

Hom.:

Bravo

AF:

0.0124

Asia WGS

AF:

0.0430

AC:

149

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 09, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

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