rs172814

Positions:

• chr12-103964036-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553183.5(UQCC6):​c.-11+1480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,788 control chromosomes in the GnomAD database, including 1,594 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 0.14 (1594 hom., cov: 30)
• Consequence: UQCC6 ENST00000553183.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

Genes affected

UQCC6 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UQCC6	XM_017019917.3	c.-11+1480A>G		intron_variant			XP_016875406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCC6	ENST00000543740.6	n.180+1480A>G		intron_variant		1
UQCC6	ENST00000553183.5	c.-11+1480A>G		intron_variant		3		ENSP00000446981.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20910 AN: 151672 Hom.: 1590 Cov.: 30

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 20929 AN: 151788 Hom.: 1594 Cov.: 30 AF XY: 0.133 AC XY: 9846 AN XY: 74182

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.146

Alfa AF: 0.155 Hom.: 2334

Bravo AF: 0.147

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs172814; hg19: chr12-104357814;