Variant chr12-103957073-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE
UQCC6	NM_001135570.3 linkuse as main transcript	c.-15A>T	5_prime_UTR_variant	1/3	ENST00000378090.9
UQCC6	XM_011538718.4 linkuse as main transcript	c.-942A>T	5_prime_UTR_variant	1/5
UQCC6	XM_017019916.3 linkuse as main transcript	c.-11+67A>T	intron_variant
UQCC6	XM_017019917.3 linkuse as main transcript	c.-10-325A>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCC6	ENST00000378090.9 linkuse as main transcript	c.-15A>T		5_prime_UTR_variant	1/3	1	NM_001135570.3	P1

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

Gnomad4 AFR exome

AF:

0.565

Gnomad4 AMR exome

AF:

0.445

Gnomad4 ASJ exome

AF:

0.419

Gnomad4 EAS exome

AF:

0.468

Gnomad4 SAS exome

AF:

0.349

Gnomad4 FIN exome

AF:

0.278

Gnomad4 NFE exome

AF:

0.309

Gnomad4 OTH exome

AF:

0.359

GnomAD4 genome

AF:

0.402

AC:

61150

AN:

152084

Hom.:

13353

Cov.:

AF XY:

0.400

AC XY:

29730

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.566

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.425

Gnomad4 EAS

AF:

0.466

Gnomad4 SAS

AF:

0.334

Gnomad4 FIN

AF:

0.278

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.392

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

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over