rs8115394

chr20-35302547-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The 20-35302547-C-G variant causes a downstream gene change. The variant allele was found at a frequency of 0.26 in 152,076 control chromosomes in the GnomAD database, including 5,550 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 0.26 (5550 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: UQCC1 NM_018244.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.94

Genes affected

UQCC1 (HGNC:15891): (ubiquinol-cytochrome c reductase complex assembly factor 1) This gene encodes a transmembrane protein that is structurally similar to the mouse basic fibroblast growth factor repressed ZIC-binding protein. In mouse this protein may be involved in fibroblast growth factor regulated growth control. In humans, polymorphisms in this gene are associated with variation in human height and osteoarthritis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCC1	NM_018244.5			downstream_gene_variant		ENST00000374385.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCC1	ENST00000374385.10			downstream_gene_variant		1	NM_018244.5	P1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39515 AN: 151954 Hom.: 5550 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.260 AC: 39516 AN: 152072 Hom.: 5550 Cov.: 32 AF XY: 0.262 AC XY: 19442 AN XY: 74336

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.269

Alfa AF: 0.284 Hom.: 801

Bravo AF: 0.246

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	23
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8115394; hg19: chr20-33890350;