Variant 8-96230890-G-GATTCAGTAGTT 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.*164_*165insAACTACTGAAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.015 in 800,428 control chromosomes in the GnomAD database, including 133 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.015 ( 26 hom., cov: 33)

Exomes 𝑓: 0.015 ( 107 hom. )

Consequence

UQCRB
NM_006294.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.161

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 8-96230890-G-GATTCAGTAGTT is Benign according to our data. Variant chr8-96230890-G-GATTCAGTAGTT is described in ClinVar as [Likely_benign]. Clinvar id is 1187612.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0148 (2250/152242) while in subpopulation NFE AF= 0.0214 (1455/68004). AF 95% confidence interval is 0.0205. There are 26 homozygotes in gnomad4. There are 1017 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 26 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
UQCRB	NM_006294.5 linkuse as main transcript	c.164_165insAACTACTGAAT	3_prime_UTR_variant	4/4	ENST00000287022.10
UQCRB	NM_001199975.3 linkuse as main transcript	c.164_165insAACTACTGAAT	3_prime_UTR_variant	5/5
UQCRB	NM_001254752.2 linkuse as main transcript	c.214_215insAACTACTGAAT	3_prime_UTR_variant	5/5
UQCRB	NR_045639.2 linkuse as main transcript	n.805_806insAACTACTGAAT	non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRB	ENST00000287022.10 linkuse as main transcript	c.164_165insAACTACTGAAT		3_prime_UTR_variant	4/4	1	NM_006294.5	P1	P14927-1

Frequencies

GnomAD3 genomes

AF:

0.0148

AC:

2252

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00418

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0210

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00528

Gnomad MID

AF:

0.0287

Gnomad NFE

AF:

0.0214

Gnomad OTH

AF:

0.0167

GnomAD3 exomes

AF:

0.0135

AC:

2155

AN:

160160

Hom.:

AF XY:

0.0133

AC XY:

1138

AN XY:

85698

show subpopulations

Gnomad AFR exome

AF:

0.00243

Gnomad AMR exome

AF:

0.0110

Gnomad ASJ exome

AF:

0.0480

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00226

Gnomad FIN exome

AF:

0.00526

Gnomad NFE exome

AF:

0.0199

Gnomad OTH exome

AF:

0.0204

GnomAD4 exome

AF:

0.0151

AC:

9765

AN:

648186

Hom.:

107

Cov.:

AF XY:

0.0146

AC XY:

5064

AN XY:

346058

show subpopulations

Gnomad4 AFR exome

AF:

0.00344

Gnomad4 AMR exome

AF:

0.0122

Gnomad4 ASJ exome

AF:

0.0499

Gnomad4 EAS exome

AF:

0.0000307

Gnomad4 SAS exome

AF:

0.00211

Gnomad4 FIN exome

AF:

0.00782

Gnomad4 NFE exome

AF:

0.0181

Gnomad4 OTH exome

AF:

0.0175

GnomAD4 genome

AF:

0.0148

AC:

2250

AN:

152242

Hom.:

Cov.:

AF XY:

0.0137

AC XY:

1017

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00416

Gnomad4 AMR

AF:

0.0210

Gnomad4 ASJ

AF:

0.0476

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00528

Gnomad4 NFE

AF:

0.0214

Gnomad4 OTH

AF:

0.0165

Alfa

AF:

0.0211

Hom.:

Bravo

AF:

0.0160

Asia WGS

AF:

0.00318

AC:

AN:

3478

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

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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