dbSNP rs703657: UQCC6:c.-15A>T (chr12-103957073-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001135570.3(UQCC6):c.-15A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 329,302 control chromosomes in the GnomAD database, including 24,455 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 13353 hom., cov: 32)

Exomes 𝑓: 0.34 ( 11102 hom. )

Consequence

UQCC6
NM_001135570.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

8 publications found

Variant links:

Genes affected

UQCC6 (HGNC:34450): (ubiquinol-cytochrome c reductase complex assembly factor 6) Involved in mitochondrial respiratory chain complex III assembly. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

UQCC6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UQCC6	NM_001135570.3 link	c.-15A>T	5_prime_UTR_variant	Exon 1 of 3	ENST00000378090.9	NP_001129042.1	Q69YU5
UQCC6	XM_011538718.4 link	c.-942A>T	5_prime_UTR_variant	Exon 1 of 5		XP_011537020.1
UQCC6	XM_017019916.3 link	c.-11+67A>T	intron_variant	Intron 1 of 2		XP_016875405.1	Q69YU5
UQCC6	XM_017019917.3 link	c.-10-325A>T	intron_variant	Intron 1 of 2		XP_016875406.1	Q69YU5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC6	ENST00000378090.9 link	c.-15A>T		5_prime_UTR_variant	Exon 1 of 3	1	NM_001135570.3	ENSP00000367330.4		Q69YU5

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61092

AN:

151966

Hom.:

13338

Cov.:

show subpopulations

Gnomad AFR

AF:

0.566

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.387

GnomAD4 exome

AF:

0.343

AC:

60861

AN:

177218

Hom.:

11102

Cov.:

AF XY:

0.342

AC XY:

31962

AN XY:

93492

show subpopulations

African (AFR)

AF:

0.565

AC:

3357

AN:

5942

American (AMR)

AF:

0.445

AC:

3793

AN:

8516

Ashkenazi Jewish (ASJ)

AF:

0.419

AC:

2196

AN:

5242

East Asian (EAS)

AF:

0.468

AC:

4445

AN:

9502

South Asian (SAS)

AF:

0.349

AC:

8593

AN:

24656

European-Finnish (FIN)

AF:

0.278

AC:

2641

AN:

9510

Middle Eastern (MID)

AF:

0.450

AC:

353

AN:

784

European-Non Finnish (NFE)

AF:

0.309

AC:

31811

AN:

102828

Other (OTH)

AF:

0.359

AC:

3672

AN:

10238

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1882

3765

5647

7530

9412

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.402

AC:

61150

AN:

152084

Hom.:

13353

Cov.:

AF XY:

0.400

AC XY:

29730

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.566

AC:

23466

AN:

41480

American (AMR)

AF:

0.438

AC:

6692

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.425

AC:

1471

AN:

3460

East Asian (EAS)

AF:

0.466

AC:

2411

AN:

5170

South Asian (SAS)

AF:

0.334

AC:

1606

AN:

4812

European-Finnish (FIN)

AF:

0.278

AC:

2937

AN:

10574

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.313

AC:

21250

AN:

67990

Other (OTH)

AF:

0.392

AC:

825

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1763

3525

5288

7050

8813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.365

Hom.:

1319

Bravo

AF:

0.422

Asia WGS

AF:

0.419

AC:

1458

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.3

(source)

DANN

Benign

0.78

PhyloP100

-1.2

PromoterAI

-0.13

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over