rs322107

Variant names:

• chr12-103964553-G-A
• rs322107
• ENST00000543740.6:n.180+963C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000543740.6(UQCC6):​n.180+963C>T 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 152,158 control chromosomes in the GnomAD database, including 1,595 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 (1595 hom., cov: 32)
• Consequence: UQCC6 ENST00000543740.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UQCC6	XM_017019917.3	c.-11+963C>T		intron_variant	Intron 1 of 2		XP_016875406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC6	ENST00000543740.6	n.180+963C>T		intron_variant	Intron 1 of 2	1
UQCC6	ENST00000553183.5	c.-11+963C>T		intron_variant	Intron 1 of 2	3		ENSP00000446981.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20946 AN: 152040 Hom.: 1591 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0914

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: 20965 AN: 152158 Hom.: 1595 Cov.: 32 AF XY: 0.133 AC XY: 9870 AN XY: 74396

African (AFR) AF: 0.121 AC: 5019 AN: 41506

American (AMR) AF: 0.199 AC: 3047 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4830

European-Finnish (FIN) AF: 0.0914 AC: 968 AN: 10594

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10308 AN: 67988

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.144 Hom.: 209

Bravo AF: 0.147

Asia WGS AF: 0.0470 AC: 165 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	1.7
DANN	Benign	0.64
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs322107; hg19: chr12-104358331;