chr12-103964036-T-C

Variant names:

• chr12-103964036-T-C
• rs172814
• ENST00000543740.6:n.180+1480A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553183.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCC6	ENST00000543740.6	TSL:1	n.180+1480A>G		intron	N/A
	UQCC6	ENST00000920803.1		c.-11+1480A>G		intron	N/A	ENSP00000590862.1
	UQCC6	ENST00000553183.5	TSL:3	c.-11+1480A>G		intron	N/A	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

African (AFR) AF: 0.121 AC: 5005 AN: 41348

American (AMR) AF: 0.200 AC: 3040 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5176

South Asian (SAS) AF: 0.0705 AC: 340 AN: 4822

European-Finnish (FIN) AF: 0.0913 AC: 958 AN: 10492

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

European-Non Finnish (NFE) AF: 0.152 AC: 10307 AN: 67962

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.151 Hom.: 4152

Bravo AF: 0.147

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.74
PhyloP100		-0.29
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: rs172814; hg19: chr12-104357814;