20-35308144-C-T

Variant names:

• chr20-35308144-C-T
• rs6058227
• NM_018244.5:c.652-1365G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UQCC1	NM_018244.5	c.652-1365G>A		intron_variant	Intron 8 of 9	ENST00000374385.10	NP_060714.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC1	ENST00000374385.10	c.652-1365G>A		intron_variant	Intron 8 of 9	1	NM_018244.5	ENSP00000363506.5

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

African (AFR) AF: 0.281 AC: 11660 AN: 41512

American (AMR) AF: 0.0862 AC: 1319 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3472

East Asian (EAS) AF: 0.170 AC: 881 AN: 5188

South Asian (SAS) AF: 0.306 AC: 1477 AN: 4834

European-Finnish (FIN) AF: 0.0790 AC: 838 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5687 AN: 68018

Other (OTH) AF: 0.137 AC: 290 AN: 2116

Alfa AF: 0.117 Hom.: 385

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
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6058227; hg19: chr20-33895947;