rs6058227

chr20-35308144-C-T

Variant summary

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

The NM_018244.5(UQCC1):c.652-1365G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,260 control chromosomes in the GnomAD database, including 2,369 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 0.15 (2369 hom., cov: 33)
• Consequence: UQCC1 NM_018244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCC1	NM_018244.5	c.652-1365G>A		intron_variant		ENST00000374385.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCC1	ENST00000374385.10	c.652-1365G>A		intron_variant		1	NM_018244.5	P1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22544 AN: 152140 Hom.: 2341 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.149 AC: 22620 AN: 152260 Hom.: 2369 Cov.: 33 AF XY: 0.150 AC XY: 11155 AN XY: 74446

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.0790

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.137

Alfa AF: 0.108 Hom.: 316

Bravo AF: 0.148

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	15
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs6058227; hg19: chr20-33895947;