Genetic Variant UQCC2:c.*112C>T (chr6-33697541-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_032340.4(UQCC2):c.*112C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 763,856 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 51 hom., cov: 33)

Exomes 𝑓: 0.0024 ( 32 hom. )

Consequence

UQCC2
NM_032340.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.487

Publications

1 publications found

Variant links:

Genes affected

UQCC2 (HGNC:21237): (ubiquinol-cytochrome c reductase complex assembly factor 2) This gene encodes a nucleoid protein localized to the mitochondria inner membrane. The encoded protein affects regulation of insulin secretion, mitochondrial ATP production, and myogenesis through modulation of mitochondrial respiratory chain activity. [provided by RefSeq, Oct 2012]

UQCC2 Gene-Disease associations (from GenCC):

mitochondrial complex III deficiency
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
mitochondrial complex III deficiency nuclear type 7
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

UQCC2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 6-33697541-G-A is Benign according to our data. Variant chr6-33697541-G-A is described in ClinVar as Benign. ClinVar VariationId is 1250225.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032340.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCC2	NM_032340.4	MANE Select	c.*112C>T		3_prime_UTR	Exon 4 of 4	NP_115716.1	Q9BRT2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UQCC2	ENST00000607484.6	TSL:1 MANE Select	c.*112C>T	3_prime_UTR	Exon 4 of 4	ENSP00000476140.1	Q9BRT2
UQCC2	ENST00000887986.1		c.*112C>T	3_prime_UTR	Exon 4 of 4	ENSP00000558045.1
UQCC2	ENST00000887985.1		c.*30+82C>T	intron	N/A	ENSP00000558044.1

Frequencies

GnomAD3 genomes

AF:

0.0156

AC:

2381

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0525

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00752

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000808

Gnomad OTH

AF:

0.0139

GnomAD4 exome

AF:

0.00239

AC:

1460

AN:

611532

Hom.:

Cov.:

AF XY:

0.00207

AC XY:

660

AN XY:

319280

show subpopulations

African (AFR)

AF:

0.0537

AC:

859

AN:

15992

American (AMR)

AF:

0.00591

AC:

114

AN:

19280

Ashkenazi Jewish (ASJ)

AF:

0.000882

AC:

AN:

14734

East Asian (EAS)

AF:

0.00

AC:

AN:

33698

South Asian (SAS)

AF:

0.000245

AC:

AN:

48992

European-Finnish (FIN)

AF:

0.000250

AC:

AN:

35934

Middle Eastern (MID)

AF:

0.00399

AC:

AN:

2256

European-Non Finnish (NFE)

AF:

0.000718

AC:

294

AN:

409258

Other (OTH)

AF:

0.00478

AC:

150

AN:

31388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

129

193

258

322

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0157

AC:

2393

AN:

152324

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

1161

AN XY:

74494

show subpopulations

African (AFR)

AF:

0.0526

AC:

2186

AN:

41562

American (AMR)

AF:

0.00751

AC:

115

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.000865

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.000414

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000809

AC:

AN:

68022

Other (OTH)

AF:

0.0137

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

116

233

349

466

582

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0170

Hom.:

Bravo

AF:

0.0183

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.49

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over