chr20-35326405-A-G

Variant names:

• chr20-35326405-A-G
• rs6060373
• NM_018244.5:c.574-11640T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_018244.5(UQCC1):​c.574-11640T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,096 control chromosomes in the GnomAD database, including 19,380 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 0.48 (19380 hom., cov: 32)
• Consequence: UQCC1 NM_018244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.55
• Publications: 81 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UQCC1	NM_018244.5	c.574-11640T>C		intron_variant	Intron 7 of 9	ENST00000374385.10	NP_060714.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC1	ENST00000374385.10	c.574-11640T>C		intron_variant	Intron 7 of 9	1	NM_018244.5	ENSP00000363506.5

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73110 AN: 151978 Hom.: 19318 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.481 AC: 73226 AN: 152096 Hom.: 19380 Cov.: 32 AF XY: 0.483 AC XY: 35930 AN XY: 74360

African (AFR) AF: 0.710 AC: 29465 AN: 41474

American (AMR) AF: 0.360 AC: 5500 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1470 AN: 5172

South Asian (SAS) AF: 0.560 AC: 2699 AN: 4820

European-Finnish (FIN) AF: 0.453 AC: 4789 AN: 10582

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26286 AN: 67970

Other (OTH) AF: 0.463 AC: 978 AN: 2114

Alfa AF: 0.413 Hom.: 53695

Bravo AF: 0.475

Asia WGS AF: 0.521 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.86
PhyloP100		3.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs6060373; hg19: chr20-33914208;